CupcoI only look for each variant once. I'm playing Pokemon with the codex. There are other variants of bacterium that can be camouflage as well. The dark planets are the worst and waiting for a ping on the SRV composition scanner can be a wild goose chase, particularly since bacterium likes flat areas and the scanner only hits areas above the flat where there is some topography.
I've found several on slopes or in the mountains but yes, most of the time they like the flat terrain. I always look on the daytime side of a planet but if it is too far away from the star it is dark anyway. I don't have an SRV with me right now. I am just checking systems as I make my way back to the bubble.