How to tell the difference...

[StormcloakNord]

Between pup whining for the sake of whining in the crate and actually needing out?

It seems a solid 50/50 at the mo. Sometimes he'll sniff and pee/poop straight away so obv needed out, other times he'll just start playing about and clearly doesn't need a pee!

He's just coming up for 16 weeks and he's slept through the night previously... is it just a case of doing it every time until he definitely sleeps through or?

I'm so tired

I think you observe for a couple of nights, how often and what sort of time span between wee/ poops & then use that to guess.
Make sure he has wee’d before bedtime and has had whatever is normal number of poops in a day.
Sounds like he’s trying it on a bit to get the attention & they quickly learn that they get a reaction from you. Little buggers.