You can find them all over the place one or two at a time. You can also easily save scum to avoid using some of them, especially living tools. Save, open the room/container to see what is there. If it's not worth using the tool, just reload.

I swear I remember seeing a loading screen tip or something that told me to not be afraid of using them,and that I'll get more

Imagine having necessary consumables in a game without a way to consistently replenish them.
Lanterns, however, seem to have infinite stock at most shops that sell them.

in geneforge 1 mutagen, do the shops ever refresh?