I think that tube you pictured, with the cap, is supposed to be opened occasionally to drain any oil and water that has accumulated.
Emissions crap is right. Crankcase breather, to a vapor collector..?, to the airbox and drain.
It was a fallout collector for a crank case ventilation system. Supposedly the system would allow condensation of oil and water vapors before passing "cleaner" air out. You need to occasionally open the cap and drain out the crud, and probably stick a pipe cleaner up there to clean out the tube. Newer Hondas use it too, sich as my wife's 2007 Metropolitan. (Can I say Metro on this board?)
(edit) oops just saw Kirrby gave the same answer, only shorter.