Well AFAIK they should not, I just did a test and you are correct they do still get exported!.
I just found another thread on this
Which is inconclusive as far as I can see in what really should be happening.
I also had a look at the Advanced export but could no stop the export of an (eye) hidden element there that I could see.
Did you manage to find out what should happen when exporting (eye) hidden elements.?
Cheers.