Random items become invisible, to make the number of visible items stay at 500.
You can remove a number of items, close, reopen storage and a number of random items will reappear.
But it is best just to use vehicles or storage boxes to reduce item counts and keep storage organized.
Before having to buy extra containers: The item limit applies per storage domain, so you could transport them elsewhere where you don't need the space. Arkadia Moon or Underground would be the logical choice as this is where these items are used, but CP, Asteroid or Thule also do the trick if that's closer to where you normally play.
I have notified Arkadia team if something can be done about it, pretty sure this was not intended to cause problems.
i store stuff over 500 on other planets - stuff i dont need or want like starter pack items - i store on planets i dont got to much - i would also suspect that MA never did code for this - bwahahaha now you know wheres the memory leak !!!