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Bacteria probably woun't affect them, you're right. But say a bacterial culture like fungus begins to grow, then even they would have issues. They could displace joints, make their energon/oil/what ever tainted enough so that it couldn't be used and cause other maladies. A metal body is a very harsh place to live, but bacteria/viruses are the most adaptable things out there. If anything could live on them, it would be disease.

Assuming robots really do have 'CNA' (cybertronian dna I think it's called, an individual "blueprint"), they could have viruses. In order to have CNA, they would have to have cells with some sort of nucleus, cells which are vunerable to attack. And not just "computer" viruses, but human like illness. Viruses are not actually alive, just DNA (possibly CNA) altering fragments that are picked up by living cells (accidentally or not). The virus then "changes" the host cell, forcing it to produce more viruses, instead of doing what it's suppose to. Kind of like reprogramming it and kind of like revenge of the body snatchers, except viruses to not eat, sleep, drink or do anything else that would be a life process... It kinda creeps me out.