This subject comes up pretty often;
here are most of my thoughts on the subject.
If asked to measure the overall difficulty of the game I will make the assumption that the player does not deliberately play badly or have any huge misconceptions about the game. Therefore I would say that, for example, versions 0.5 and earlier become much easier than any later version as soon as the player picks up a spellbook containing Detect Creatures (a level 1 spell that gave you almost perfect knowledge of almost every monster on your level). An early-game difference will also obviously dwarf any difference in difficulty that happens after the first few dungeon levels, so since detect creatures wasn't in any starting books (?) the example I gave is not really that great of a claim for 0.5 being easier unless, again, you assume deliberately poor play (increasing the relevance of non-early game "difficulty"). You could probably argue things either way (-heavy armour -floor item enchantment -some starting equipment; +starting hp +skill costs +some starting equipment).
If we are also only looking at the strongest character combination* then the addition of DD is possibly relevant since it is possibly as good or better than Ce (no other species comes anywhere close, and Ce has been basically the same since forever).
*Looking at only the strongest combo is a reasonable assumption in my opinion, but if you think character combos should act as "difficulty levels" then it is possibly not a good one to make, since almost all games with difficulty levels are extremely easy on the lowest one. Judging difficulty based off of MuCK doesn't sound very good either though.