The cracked multiport valve won't effect the pump's suction while it's operating, but once the motor shuts off, then it will let air "in" which causes water to move within the plumbing and perhaps empty that pump pot. A pool's plumbing system needs to be air-tight to keep everything (water) where it was, including the pump pot.
As for the pump pot water level, some VSPs simply don't fill all the way, or perhaps stay that way, all the time. Most common is for a VSP owner to ramp-up the rpms once or twice a day to purge air that may have collected under the lid. They usually fill to the top on an high rpm. Most importantly is that during normal operation it doesn't drop so far that you lose prime to the pump because water helps to keep the pump cool. Definitely check those drain plugs next chance you get. All those places where air can get sucked "in" at or before the pump will influence the amount of air in the pump pot.