Can't comment on the wire bonding quality but yes you're not supposed to sonic wash anything with an oscillator. This includes ultra and mega sonic. I had always thought it was because you could damage the crystal or mems structures, so color me surprised to see this failure mode, though there still could be a shift in frequency that the scoping wasn't able to see.

I tried looking at an exemplar ECS tcxo datasheet and didn't see anything in there about washing which is surprising but it also doesn't say not to crush it with a hammer so maybe it was assumed. That's bad on them.

As for SMA to 0.1" headers: yes these are very cursed. But RF designers love putting SMAs for every connector on an eval board (power, enable, whatever) and those come in handy.