Aft deck drains clogging are industry wide issue. solution potential has to do with what is clogging them, how big the drains are etc.
many drain types are avail, here is a company that makes a few.
http://www.marineeast.com/a_sch/sch_lst.asp?cid=2be careful of unscuppered straight drains as water can flow back up them turning them into fills instead of drains, incoming water will push past debris but debris will act like a valve and not let it back out.
other possible non perfect solutions are wire cages covering top , switching to larger unfiltered drains and inline scuppers (th marine 1.5"), installing aditional larger drain sytems, etc.
thought i saw one boat that had small stainless baskets that were siliconed over drains, seemed to work well. they looked like they came from a 99c store or target. woudl wworkwith plastic also, just a few dabs of siliconeto hold in place, easily removeable, a lot elss likely to clog than my ping pong ball drains imho.
I had trouble in past with pieces of celophane,& paper from tackle packages, fishing line clips, snack debris and fish scales making a mat over the drain, Now ive instituted crew "drain awareness training" and trash containment bags things have been much better.