Well, if he want to get a new weapon, he had to ditch the current one. (once again, there's always that slot limitation)
For example, he had shoulder beam cannons, and no empty slot to add a Gatling weapon mid fight. He had to destroy that cannon from database to assimilate that Gatling.
There's a big downside to this, we all knew that I.S. parts gather experience overtime, and destroying the parts from database means you lost a leveled up weapon forever.
