I just left what was remaining when I bought my boat 6 years ago in place. I believe the part is called a cap but from what I have seen doesn't provide a seal, no weather stripping. All 2400 SCR's I have seen it is either broken or gone. I doubt any issues would exist if missing.
I have a mooring cover on my boat that goes from the top of he windshield to the transom and keep the boat in an open but covered high and dry so i don't get any water on it to determine if would leak.
FYI: part number and description 56981 ENTRY HATCH CAP
1997 2400 SCR
5.7 Vortec / Bravo 2