I had something VERY similar! In my case it's my dd (nearly 6) who HATES the calls, and would throw the phone/cry/ refuse to talk etc. My ds (nearly 2) likes the phone on the other hand!
I got exactly the same response as you (I was blocking the calls/ didn't want him to contact them/ I was told they "needed" the consistency and he would not stop the calls) He also insisted on calling at 6pm every night, just when we were starting baths etc etc despite me repeatedly telling him they were too tired and it wasn't a good time to call and could he try earlier. And like your ds my dd got a bit of a guilt trip about not wanting to talk.
Not very helpful in your case but I eventually managed to persuade him to call them at their childminder's in the week so the calls could be earlier. My childminder bribes my dd with various games etc to talk, and says she just repeats a "hello daddy have you had nice day? I've had a nice day. I'm going now" type of conversation and gets it over with. My ds then has the phone until it gets cut off.
When he rings here now, I ask dd if she wants to talk, but I don't get stressed about it any more. I just say "she doesn't want to talk" if she says no and leave it at that. She's stopped getting quite so anxious and upset now she doesn't "have" to speak, and sometimes she will talk.
I think I'd tell your ex that you will ask your ds if he wants to talk and just calmly tell your ex he doesn't want to if he refuses. Try not to get drawn into the emotional stuff. Agree it's hard for your ex if he doesn't want to talk, but say you're sure he'd rather your son wasn't getting upset. I'd put it all in writing too - just saying that your son is very upset at the nightly calls and asking him how you think it should be dealt with. That way you have a record both of your concerns and that you're trying to sort it out with your ex.
My dd doesn't like talking to me on the phone either. So much so I stopped calling her and I just text now. But I got accused of "not feeling bothered" about calling them 