Are there any special rules for droids in regards to built in armor or built in weapons? (I didn't find anything in the books so far but maybe I have overlooked something or there are some commonly used houserules there?)

mostly it's figured it's either built into the droid or when they pick up something new can be integrated.

In my games it's a small fee (usually like 200 credits) to add or take out since our group doesn't have a mechanic to mod the droids on our team.

so normal armours just "flavor" beign built in.

pretty much, when a droid upgrades their armor it's just bulking themselves up.

Yeah, with things like armor, its just "heavy plating" added. Cost, encumbrance, and other qualities are identical to meatbag armor of an equal type.

Tools again are the same, identical to the meatbag version, it just pops out of a hatch instead of being pulled out of a pocket. Still has the same cost, enc, effects and so on. Still requires a maneuver to take out and put away.

Weapons the same. Per RAW it still has to be pulled and holstered same as any weapon (even if its externally mounted) reloaded when it runs out of ammo, and so on.