So I will be adding a subwoofer and amp to my 2021 ES 350 non ML system. Does anyone know what speakers are in the rear deck is it just 1 sub? Should I disconnect it if adding a sub?

 

Just one sub back there, no proper speakers

 

Crutchfield says that a 10" sub will fit where the stock hole sits.
The challenge will be amplification. The stock unit has insufficient amounts of power. I doubt the head unit has pre outs for an external amp. You will likely have to get an external amp and use the high level input from the factory leads that connects to the subwoofer.
I'm not a bass head so the stock amps and speakers are good enough for me.

 

Yes, you'll have to use high level inputs going to the stock sub if adding an amp. When I installed a JL Audio 10w6v3, I learned very quickly that even the ML system puts out a weak amount of power. I'd assume the stock system is even less. So you'll definitely want an amp.

Also, you'll need to turn off the Active Noise Cancellation (ANC) if installing an amp. ANC does not play nice with aftermarket amps. You'll hear a constant hum if you don't. Carista is the best way to make that change in the ECU.