As for Lucrezia watching something for 500 years... she's functionally immortal and signs point to her sanity being a little... frayed.

At best.

Also, I suspect that Agatha's little clanks having the spark is something new, and there's no reason to assume that Lucrezia has any knowledge of it or how to do it. My read is also that machines in the GG universe mostly can't be sparky, not just can't be queens.