This sounds like you're overheating... overheating can damage your modules, including your cargo hold. Is it possible you're also overheating when fighting elite Anacondas because you're firing weapons for a long time? or firing SCBs?
Overheating will indeed do the trick.
Using a shield cell bank in combat will damage your modules and every subsequent use will damage them a bit more.
The cargo hatch is always the first to pop in my experience.
I can use two shield cells. When I use the third my hatch pops and cargo spills out.
I have lost some very precious engineer commodities that way, because I was forced to go into combat zones to get some materials and had no way to store the engineers commodities I already had collected in my hold.
This is one of the reasons I want to be able to store my engineers commodities.