No-one forces you, the choice is yours:
Seek out HGE-s (boring, but fast),
Or sacrifice 2 optional slots on your PvE ship, which is completely OP against NPC-s anyway, to pick up phat loot from that pirate lord ship you were sent to assassinate,
Or stop rampaging through RES-s like an absolute maniac and take some time to smell the ashes and savor the moment while picking clear the bones of your enemies (where's the hurry, you need to wait for new targets to drop in and your shield to recover, anyway),
Or do missions that reward materials, ignoring all the loot your targets drop.
Enemies dropping loot has been a staple of all games ever, it's up to the player to either go rummaging through the pile of corpses or ignore all that and find an alternate way to get stuffz. For the record, I also ignore low level mook possessions after a certain point, but they are an invaluable resource during the early game.