Grumpy, Had look up the emulsifier tube description here as we call it a nozzle but yes most times the plastic version are just left in place when cleaning. I still remove them later if I think replacement of the o-rings is needed.
On carburetors with the removable brass nozzles I usually leave them in place too except I do remove them later just for inspection but that is just the way I learned how clean carburetors over the years. This is just the same way I adjust OHV valves which is different than what is in the service manual.
For those that don't normally work on carburetors these removable brass nozzles are usually damage by previous techs using the improper tools to attempt to removal of these. Regular flat blade screwdrivers don't work on these. The flat screwdrivers must have straight sides just a little narrower than threaded part, be hollowed ground, and be of the correct thickness.
As for cleaning carburetors in my cleaner I have even left stuck on gaskets made of gasket materials with little ill effects. I do however recommend using normal carburetor breakdowns as it is just common sense to do so as it both makes cleaning faster as it eliminate air pockets and the replaceable parts should be inspected anyway. Normally you simply leave the welch plugs in place too. In my opinion why remove them when you don't need to.
The main thing using an ultrasonic is to not over load the cleaning tank with parts or let your cleaning get too dirty before changing. On the dirty solution I use this rule. If you can't see parts near bottom of the tank the solution need changing. It sorta like washing your socks in muddy water. It removes some the dirt but it can also it behind.
With the introduction the Chinese carburetors and the lack of replacement parts you simply can't risk damaging parts that are still in good condition; unless you willing to buy a new carburetor.
Hopefully I am not too long on this as I do sometimes tend ramble about things.