I am pretty sure that the handheld bio scanner does add stuff to the Codex, I will try to confirm that tomorrow if I find anything new to me.I've read in a few places that scanning with the Comp Scanner also triggers things like the Codex acknowledging your find (and by implication the Genomics scan doesn't do that.)
Is this true? In which case this thread could be a discussion on how to make the Comp Scanner better, because it is supposed to be the tool for this in the gameplay loop and the intended solution for finding little black microbes on a black background which wiggle their little cilia when you find them.
It seems the community has decided ship plus on foot is The Way but what if The Way for bacteria is still SRV turret and Comp Scanner?