I have an ultrasonic cleaner too, but no pens were stubborn enough to necessitate a bath inside it.

I generally "power flush" my pens with a syringe: Get a 50ml syringe, cut the sealed end of a cartridge, fill the syringe, mate the syringe, cartridge, pen, and push the water through. After a couple of times, the pen is thoroughly cleaned. Shake a couple of times, let it dry.

On the other hand, many (if not most) inks have some detergents in it, and keep your pen clean and clog free as long as you use them. Older inks used Solv-X which was more effective but deemed carcinogen and banned in modern inks.