SEO-wise there's no difference other than performance. But it was possible to build high-performance SSR sites with React 15, and with React 16 it's even easier.
The more important thing to decide is whether the development model of React is suitable for your needs.
We're actually doing this right now with tylio.com. We get pretty high scores (95+) on the various test tools (Pagespeed, Lighthouse, etc.) using React 15. Our biggest remaining issues right now are First Meaningful Paint and Time to Interactive, and I expect React 16 to help a lot in that aspect (streaming render + simplified rehydrate), can't wait to test it!
The more important thing to decide is whether the development model of React is suitable for your needs.