Just wondering what they are? They have a little rubber flapper but not water tight by any means. Thanks

Can you provide pictures? If I had to guess I'd say they are drain holes for around the engine hatch

The one currently is the classifieds section shows one on the starboard side just over the drive in the pic. Either engine hatch or maybe it is to drain the inside hollow portion of the swim platform?
* Also, I found a 2003 Vyper 340 for sale but does "not" have a stepped hull? I thought they were all stepped by then, starting in model year 2000 or so? Did Powerquest
vary from stepped to non stepped per Vyper built for a few years?

There "scuppers". As for what area drains out of them I have no idea. My guess is in between swim platform. I just replaced the flap and cover on my 380.