So far as the lettering is concerned, I know EXACTLY where to look, and if I squint, with my 72-year old eyes, I THINK I can see traces - nothing clear mind you, it's 90% faith - but I still see something!  :-)

Did people "normally" remove such markings? - NO, they did NOT, and I believe such mutilation to be quite illegal at the Federal level. THAT could be the source of the 3xxx number (which, by the way, I cannot see!) having been added, probably by a gunsmith, as an alternate identifier. Another POSSIBILITY is that the gun was once stolen - MANY years ago - and the party tried to erase the marks of Government ownership? Perhaps your uncle was concerned, and had it marked when he acquired it?

As to shooting it, since you and your family have done so, I guess (though I am neither a gunsmith nor a trained metallurgist) that it is "OK". The numbered surface is not where the lockup occurs, and the Krag has that massive rib, so the bolt is never going to come out, but, at the very least I'd wear shooting glasses and stick to occasional use with moderate loads.