I would not be concerned about the extra length doing anything other than catching dirt and being a hazard to working under the trailer - for the latter reason I would consider clipping them off, but that's just me. The nails have now made holes right through the thickness of the plywood, but I don't think water coming up from the bottom has been a problem for anyone (except in a flood, and you're not stopping that water) so it doesn't seem worth worrying about.
Sleep well - I really don't think the nails are a big deal.
1979 Boler B1700RGH, pulled by 2004 Toyota Sienna LE 2WD
Information is good. Lack of information is not so good, but misinformation is much worse. Check facts, and apply common sense liberally.
STATUS: No longer active in forum.