Are the drains in the pool and spa one or two covers each (two or four total)? If it's just one in either body, that is a pretty dangerous thing to have in a pool/spa. Single drains have caused injuries and deaths. At the very least have a conversation with the contractor about converting them both to anti-entrapment systems.
For your pool/spa system to work, you need a suction port in each body of water. So that likely means you'll need to leave the drain in the spa. But the pool's suction port can be the skimmer(s), where they are much safer under the skimmer basket, so you could safely lose the main pool drain without affecting your filtration/heating setup.
I knew ahead of time that getting rid of my drains was not going to affect my pool's circulation, because the drains were plumbed to the skimmer, and the diverter plate that would have made the drains active was never installed, which means my drains never did anything in the first place. Losing them was a no-brainer for me.
Do you know? Is your pool drain plumbed to the skimmer, or back to your pad on it's own dedicated valve? Has your pool drain ever been used for circulation? If not, ditch it. If you've been using it, then you'll have to consider how getting rid of it will affect your pool's circulation. Drains don't do much for circulation, that's mostly done by the returns. Pushing water around a pool is way more effective than pulling water through some holes (like a drain). Once I got my eyeballs, I adjusted them to create a nice whirlpool affect in my pool, and that solved for the warm/cold spots I'd always had, so my circulation actually improved after getting rid of the drains, because of the returns.
It was my remodel contractor that suggested getting rid of the drains. They explained all that to me before I did, and it worked out great. Perhaps your contractor can assess your circulation system and advise you similarly.
Alternately, if the main drain is plumbed back to the pad, you could leave it as is, and just turn it off. If that leaves your circulation OK, then leave it like that and make your pool safer that way.
Or use one of these, they're anti-entrapment and hide the drain pretty well. You can plaster over their covers to make them virtually disappear (but they still work as drains). They make dual-round versions, too, and there are several competing brands that make these, so lots of choices:
www.cookeindustries.com.au
Here's another:
Color Match Pool Fittings is a direct manufacturer of pool drain covers and fittings. Our Pebble Top Drain Covers blend with any pool finish and virtually disappear into your pool floor or wall.
www.poolfittings.com