I have a 9month old Bernese Mountain Dog, who until recently has been a model dog - house trained within a couple weeks even.

But recently - for the past 8 nights has been soiling himself, several times a night. However during the day, he seems absolutely fine, eating normally, and asking to go out as he would normally.

Could this be separation anxiety rather than an illness?

It could be - but you need to rule out medical cause first.
When you say soiling - is he urinating? If so, you should bring a urine sample into the vets to rule out infection. Often dogs will urinate inappropriately if they have a UTI.

No, its everything, loads of wee, poos, and even diahrea? And tonight he's woken me up twice with barking loads, and wanting to go out, barking and then coming in again...

I will be checking with the vets on Monday I think, as his companion is a much older lab ( 10 ) who displayed very erratic behavior ( scratching the doors until his paws bled and the glass fell out ) after the death of this one's predesesor? Is it possible that he's following a bad example? Despite the bad behavior stopping just a couple days after the newcomers arrival?

Take him into your vet. It could just be not being able to go anywhere. It could be a illness, or, if you aren't spending as much time with him as you did when you first got him, it could be loneliness. Talk to your vet. She/He Knows everything when it comes to animals.