I would put the block off plate on (I did it on my 750SS). If you leave the pump and run it dry it might seize and cause damage to something. If you remove the pump and don't block off the hole that's left behind you could get water and crap in the cover that it attaches to and I believe the stator is in there.
I would also get the crankcase drain block off plate while I was at it, that's one less thing to go wrong and the $30 the plate costs is a lot cheaper than rebuilding the engine. No surprise I installed that on my 750SS too.
Did you pull the pickup out of the tank? My ski would run for about 15 minutes then die. After a few minutes it'd start up and run great again. When I pulled the pickup out of my 750SS it was covered in a white corrosion that was blocking the vent and return lines. I also found both the pickup mounted filters gone and the pickup tubes split from top to bottom. I repaired the pickup tubes, cleaned the corrosion off, cleared the passages in the top of the pickup, and went to an inline filter, no more problems with it. Before I put the inline filter in I kept getting crap in the internal filter that's in the carb and its no fun pulling the carb off to clean that tiny filter out all the time. I can see all the same type of crud in the fuel filter now. I'd pull the tank and clean it out but that would require removing the engine and I'm not going through that much work. Fuel filters are cheap so I'll change my filter 10 or 20 times before I pull that motor out.
John