Yay, another Nott writer!
I'd say it's very likely that Nott Sr. would have been at school during Riddle's time there, or possibly just before...it depends on how elderly you plan on making him. If you made him, say, seventy-five when he was captured at the ministry, then he would have been starting school in 1931 and graduating in 1938. Which means he would have been in his last year when Riddle came. If I did the math right.

In my story, Theo's mum dies from a sickness, but murder opens up all sorts of possibilities. Who would kill a Death Eater's pureblood (we presume) wife, and why? Does this have anything to do with how Theo turned out? Murder could be really interesting if you plan on focusing on his parents, but it could get distracting if you don't want the readers to focus on them.

I'd say yes, the mother was much younger than Nott Sr. As far as arranged marriages...they are used so much in fanon that you could probably get away with it. Personally, I think it's been used a lot, and it would be interesting to see some other reason. Women do sometimes marry older men without being forced to.

I think out of all the Slytherins in canon, Nott is the most likely to side against the Death Eaters, as long as he has motivation. Remember that he's not naturally a follower, and this goes for the good guys as well as the bad...he's not going to just do whatever the Order tells him. He is, after all, a Slytherin, and a very clever Slytherin. He is going to do whatever benefits him, as Vorona has mentioned.