"hunger clock"
For the most part, this needs no correction; Crawl really doesn't need a clock, though hunger is more of a very lenient parking meter. There would still be piety decay to keep players moving, at the very least.
If scumming is a serious concern, I have a few suggestions. First, and most obviously, anything that currently can benefit a player who just stands still, such as Xom gifts, is moved to an XP timer or removed. Next, all monsters that spawn after a level is generated provide no XP, using whatever flavor justification works best. I prefer a system that ends these spawns when you kill the last XP-bearing enemy. When you leave a level and monsters are in LOS of the stairs, all of those monsters will patrol that staircase as long as you are off the level.
No further changes are necessary for Pan or the Abyss; players who want to scum there already can, and it's miserable, and they should be left to their devices.
vampirism
on equip, the message says "The [weapon] thirsts for blood," and the vampiric effect kicks in fairly slowly as you kill enemies ("The blood of the [enemy] coats the [weapon]"). When you unwield, "The aura of blood disappears from the [weapon]," and you start from 0.
Trog & berserk
Making berserk cause hunger isn't really a meaningful limit on the number of times you 'zerk, as there's more food than enemies that require it unless you're a Spriggan or terrible at Crawl. I'd suggest replacing it with strength draining, especially now that stat drain is on an XP timer. Trog reduces the chance of str drain with higher piety, but it's still a good chance, and you can't berserk if str falls below some threshold (half str?). This can be a really modest str drain; the goal isn't to kill players via stat zero, but to keep players from 'zerking in every encounter.
starvation penalty
The wiki says it exists, but I doubt it ever, ever matters, so just remove it.
regeneration
Regen increases hunger, but right now that doesn't matter much unless you're wasting a whole lot of time while having less than full HP. I'm inclined to just let this one go. If there needs to be a better limiting factor to regen, it should be covered by the effect itself, and not the hunger cost it levies.
notable species (Sp, Vp, Gh, Mu)
Sp
I think no change is really necessary; if Sp would be overpowered in foodless Crawl, they're overpowered right now, and if a nerf is needed, the food conduct isn't really the place. You could, of course, retain fruit for Fedhas and turn Sp into a species that will die without consuming fruit, and then tune that "hunger" level so that the game generates enough fruit for Fedhas & Sp, but that's only if you really want to maintain Sp's status as the "hunger species."
Vp
I mean, remove Vp, but if you can't, then simply leave bottling blood alone until someone comes up with a better idea for Vp. The hunger clock on Vp can be calibrated to whatever Vp players think is a good idea, and just ticks down over time. You could always make an (a)bility like "Bite," which lets Vp control their aliveness without "hunger," too.
Gh
Just make it Makhleb: The Species, honestly. If it kills things that would give it chunks now, it gets a shot of healing; if it goes too long without killing, it begins to rot away. Again, the rot timer should be balanced around whatever works for Gh.
Mu
Mummies really only get screwed on hungerless channeling and casting, which are two major advantages it doesn't get in foodless crawl. If it's thought that they need a buff, they could have some kind of +wiz or something? "Fast channeling"? Whatever, they're mummies and they're supposed to be bad, and most of these changes only increases the degree to which they're relatively bad.
spell hunger
This is probably one of the trickiest things to replace, since I think a substantial number of people feel that this is a meaningful limitation. I think they're often mistaken -- it takes bad play, a bad combo, or terrible RNG to run into a hunger wall with casting -- but it also seems as though people think this is a good limitation.
First, I'd advocate for simply not having spell hunger anymore. MP is a meaningful limitation for the number of spells you can cast at any one time; if it's felt that players can cast too many spells before resting, reduce max MP instead. If the concern is that players are using high-level spells too early, increase the XP required for higher spell levels, or require that players achieve a certain XL to cast spells of a certain level.
However, if people really want a non-MP/XL limit on spellcasting, I would suggest int drain, in a similar fashion to the way berserk causes str drain above. As your spellcasting skill and intelligence gets higher, the chance you get int drained is lower. A staff of energy prevents int drain, while Necromutation moves down to level 6 and has no effect on this draining.
channeling
The hunger cost of channeling is virtually meaningless. Strategically, there's more than enough food for any caster to channel regularly for the whole game. Tactically, I find that the limited MP you get from channeling is a lot more impactful than the hunger cost, especially since it's always easy to just scarf down a fast food item.
If channeling doesn't seem overpowered to you right now, it probably doesn't need a replacement limitation in foodless Crawl. If it's overpowered, though, I'd suggest making each channel take longer than a single turn, with high invo/evo levels required to bring it down to 10 aut.
hungry ghosts
Can just go away, thanks.
(a)bilities
No abilities really need to cause hunger, as it's not currently a serious limiting factor. If people are worried about players spamming +blink or =tele, you can increase the contam of either. If +Inv spamming is a problem, turn it into an evocable item that goes inert instead.
rods and special staves
Rod hunger (and staff of Dispater hunger, lol) is pointless, and needs no replacement. Rods are fine; I guess evocable hellfire might need to do more HP damage.
Fedhas
If people like the idea of Spriggan as a "hunger species," you could always keep fruit in the game for them and then retain Fedhas' mechanics. I've also heard people suggest that, when you pray over corpses with Fedhas, you occasionally get fruit instead of mushrooms.
I suspect it would be simpler to just make Fedhas run off piety entirely.
mutagenic chunks
I really don't think there needs to be a replacement for this. If people want to play mutation roulette, they can quaff mut pots. If it absolutely can't be lived without, anything that previously provided mutagenic corpses create a mutagenic cloud over their corpse for a few turns after death (with clouds changed to give random mutations, if they currently lean toward bad ones, I guess?). But that's pretty dumb, so, sorry mut roulette lovers.
hides
Dragons/trolls can simply drop these instead of requiring butchering. Easy!
other gods
I'm pretty sure that it's basically just Trog and Fedhas that have to be seriously looked at for foodless Crawl. Ely already basically works off piety instead of hunger, and piety costs can be adjusted for her abilities if removing hunger makes them too spammable. I guess this is also a Zin buff, since now his food conduct doesn't matter, but it's pretty minor. All other abilities that only have MP and hunger costs should probably just have higher MP costs if they're especially spammable.