It's fine. Feel free to prune your squash. You can prune stems to length or prune stems from the maim stem at the base. Do not prune more than 1/3 of the overall foliage at any one time.

Actually, I don't see that one would really affect the other. If the squash don't climb the tomatoes and just sprawl across the ground, the leaves will create a canopy that mulches the ground surrounding the tomatoes and the tomatoes will grow vertically. Therefore they can coexist just fine without intervention.

I think someone is slipping my squash crystal meth - they are freakin' humongous! I turn my back on them for five minutes and they grow a few inches.

If you're out there every day consider just pinching out the growing tips on the squash, just in the direction you don't want them to go. That works well for me. I have a vine that's encroaching on the doorstep of our family school house.

George
Tahlequah, OK