I rarely use numbers. But I also make sure there's a way to differentiate between the two.
For example, I've repainted 2 X wings, 3 Y wings, 2 A wings, and 2 B wings, which means that I have 3-4 variations of a ship (because I can also use the unpainted version, or the alt version in the case of the X)... And just in case that doesn't fulfill it completely, I'll use two different heights (the tall X wing is the top card, the short X wing is the bottom card) of the ships.
Given, if anyone asked me to, I'd gladly throw on tokens to prevent any confusion / accusations of cheating.
And the few times that I play imps and don't have any repaints, I always use numbers.
We often use the numbers to indicate pilot skill, because our table sits a little high. It also helps us never forget when a ship has Veteran Instincts on. When it comes to multiple ships, we use the front for PS and the back to differentiate between ships. Or we use the ABCD token things that came with some of the huge ships, because they all fit and we never play scenarios. Might as well use 'em for something