It is never rude to tip any amount. I suppose that there is a point at which it becomes foolish, e.g. over a penny or equivalent in non-US$, but never rude.

Whether you choose to calculate tips to the penny based on a notion rate or to calculate approximately and then round up is entirely a matter for you.

I tend to round-up to the nearest dollar on larger items and I don't leave less than $1. That's me, but I don't think of it as rude or anything other than my preferred practice.

On a side note, an employer paying someone to calculate the tips to see if someone improperly rounded up is run by a bunch of fools.