I'm working on a full bestiary for this run. I know the worms get replaced by diggers and spiders by recluses. But, is there anything else that is totally taken out of the mix when you go into hardmode?
There shouldn't be any enemies that disappear after Hardmode currently. Only one I'm a little uncertain of is the Giant Worm and its Digger HM counterpart. According to Heath04 above, it sounds like they have a small chance of appearing in HM now.
I think in the special seed "For the Worthy" only Voodoo demons appear and not regular Demons, so if playing on a special seed, its possible for some enemies that appear normally to not appear at all. My memory is hazy on if that may've been adjusted or not for 1.4.4. On a regular world though, it should always be possible to 100% the Bestiary.