rule number 1. dont screw around with planes on O.M., they are vicious.sure they might miss you the first time,don't press your luck.
the solution,dont go through shallow areas,especially near enemy ports. try to plan your route to deeper waters only. if your crew does spot aircraft,all ahead flank,and crash dive to at least 40+ meters. ( i prefer more like 60 meters). when deep enough,all stop and make like a bubble in the water, and just time compress until night when it's much safer to be surfaced.
if you must go through shallow areas near land,do so only at night when the planes aren't out scouting as much.
the sneaky thing with planes too, i noticed, is they're vengeful. if you just killed a contact in an area,there's bound to be a patrol through there very soon. kill and g.t.f.o. of there.
or do the above until night when it should be safer.
later on in the campaign,you receive dive command officers with passive abilities to help you dive faster, (i noticed mine appeared after i went up in rank) and reduce flooding,which will certainly help you out too. (they need to be in the control room for the ability to be active)
hope this helps.