Valid points;
A tax per individual would discriminate against faster reproducing or larger populace bots, (the advantage through numbers idea), although I was thinking of it as cost for upkeep. (for cells).
A tax per species, though very beguiling, would discriminate in the opposite direction perhaps. Then again, as you point out, there is a distinct advantage to have a large body and maybe the upkeep for a large body should be larger.
Doing both, as you suggested, might be a sound compromise.