Given US gun culture, I would not immediately classify "has a gun/knife" as "violent criminal". And even for people who could potentially be violent, how many of those police shootings involved a suspect that had actually drawn their weapon and/or was behaving aggressively with it? And if we're talking about self-reporting by cops, I don't think we should take their assessment of the situation at their word without some sort of corroboration.
Regardless, even if the police killed some 1000 armed people during a year, so what? 1000 is certainly a tiny sub-1% fraction of total interactions. If anything, you're only supporting my assertion that the vast majority of people the police have to deal with are non-violent and can be dealt with using non-leathal force, or little to no force at all.