The Skill section of Alien Archives says that "Creatures are assumed to have whatever tools they need to use the listed skills (such as Engineering) without a penalty."
Does this mean that if I kill a creature with Engineering as a class skill, I can loot it of tools that allow me to use Engineering without penalty, even if the creature's entry lists no such tools?
My thought would be that it's more up to the GM.
Is the creature planning on using the skill in such a way that it would need tools (or does it have the skill and thus might use it for knowledge rolls)? I would certainly assume that if the creature was going to use Engineering to tinker with something in the scenario, that it would have the necessary tools, but if it was near home (or near its ship), it might simply plan on retrieving tools from there if necessary.
Also, I could certainly see a GM applying the rules for modifying armor to tools as well. If the creature has, say, masses of tentacles rather than individual articulated limbs, you might need to modify the tools to be able to use them.
Otherwise, yeah, I would think, all things being equal, they have a tool kit. The cost is not prohibitive, and you aren't going to get rich reselling them. But if you shoot a wookie, take his toolbox!