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.