ajpm26

So I just bought this car last weekend and i've been working on making it cleaner and fixing it up since. It's got a b16a2 and lots of people have been telling me that the vent/filter on my intake and valve cover should be connected and not vented. I was wondering if this is bad and what could it potentially damage? Should I replace it right away with a hose connecting to the two?
Pic:


Also, there are two holes in the valve cover showing the timing belt. Do many people do this "mod" and should I be worried about foreign objects or anything?
Just don't want a crazy horror story to post up....
Sorry for the noobish questions.

Thanks