Hatches: Should it always just change the direction of the lemmings and never flip the sprite?
Yes. Nearly all hatches are symmetrical except for lighting and the background seen through the trapdoor. These are too subtle (especially for new players) to act as good visual indicators, so you're left with the lighting looking wrong. I don't think a visual indicator is needed in any case, since you can tell which way lemmings come out facing very easily.
In case some of the usermade styles have hatches that
would benefit from flipping, perhaps have the specification for hatches include an optional flipped sprite, and if none is present, don't flip.
Teleporters: Thanks for noticing that flipping lemmings in teleporters is still present in NeoLemmix. That's a perfect candidate to be culled. As for the actual topic at hand: As the sprite is the only way for the player to tell in advance whether the teleporter flips lemmings or not, I strongly prefer to keep this visual clue.
But again that doesn't work with teleporters that are symmetrical except for lighting (don't know if there are any). It's also confusing for new players, since they haven't gotten used to one orientation being the default, and this has to be learned separately for every type of teleporter.
Just cull....