It makes sense regarding game optimisation, and I've used them interchangeably by mistake from time to time. Why not?
The only thing I can think of is that if you're mis-hitting one of the two keys you might mean something else entirely (like ?) but the chances of that happening -on- a staircase are fairly low. Can't see it being a problem anywhere but the ID and Challenge mode, even then.

One answer might be if you press >> twice accidentally, as it is right now you don't end up going back up the stairs again. This might especially bother someone in the ID, when it means they just lost the level. On the other hand, that's not a really big problem, so I voted for it.

Maybe one thing you could do is bind < and > to a "use stairs" command, and then have "go down stairs" and "go up stairs" commands that aren't bound to any keys by default. Then if a player wanted the old behaviour, they could just modify the .kbd to bind < to "go up" and > to "go down".

Seconding wheals here - if they're interchangeable then there should be some kind of protection against >> and <<

Actually, the usage of < and > interchangeably might break the controlled teleport to stairs?

It's not common, but I've sometimes, say, navigating to the up staircase when I wanted to go down and then hit the down key and realized I was at the wrong staircase. So, I do like the current differentiation and second wheals's comment about rebinding.

I agree with it too.

Hm, I thought about it too but I'm sick with this even more: sometimes I'm going several level in a wrong direction and only then realising I'm getting down instead of getting up. :D I'm just always pressing key corresponding to the symbol.

How about compromise? Add a new command (use stairs) which would be set by default to < and >. If anyone likes the old system he would be able to change .kbd.

I'm giving preference to the new command since in NotEye it's harder to choose wrong stairs and mostly NotEye, not console version, will be attracting new players.

The distinction between < and > is also important when used in combination with the 'w' command to auto-go to the stairs of a direction, as with controlled teleport, as mentioned above. While I'm sure it's possible to have them remain and change only the actual move up/down stairs command it creates a bit of control weirdness where you'd w< and then could press > to go up. Personally, I'd not be in favour of changing it, it's a pretty well established roguelike convention. However, as a completely new single button to 'traverse stairs' and/or condensing both mouse actions into a single one, I think it would be fine.

Some time having passed I also have to think about it once more.