Real life is full of plot holes.
Those aren't plot holes: they're holes in your knowledge. Reality is perfectly consistent.
Knowing that there are letters designating a name, and knowing what the muck was, which it's hardly a stretch to assume (certainly Ilia would have known), one would know that maybe there was something to see by wiping the muck off.
Or maybe V'Ger, like me, doesn't give a hoot about it. Seriously, it's near-omnipotent. Why should it really mind ? This part of the plot really bothers you ? I mean, now that you guys mentioned it, you made me realise that I don't care about it, and that's all.