Netlify redirects are redirects via header, Hugo redirects load the page first, then the page redirects. So you should always use Netlify redirects if you can, they will save some milliseconds.
We will use the same domain with different sitemap, so using Hugo aliases seems allowable. But the performance advantage definitely prevails, so we’ll stick to Netlify redirect based upon the above explanation.
For the Hugo docs site we use Netlify redirects. I added it mainly to test/demonstrate Hugo Output Formats, but 301 (aka Netlify) redirects should be more SEO friendly. Don’t ask me details …
If you want to mix you would typically need to add some other page param for the Netlify redirects and generate the _redirect file from that.
The advantage of Hugo aliases is that they are easier to test outside of Netlify, but you can probably get that by a custom develpoment config.
Here’s what Google says about the redirects that Hugo aliases uses:
This (…) sends the user to a new URL after a certain amount of time, and is sometimes used as a simple form of redirection. However, it is not supported by all browsers and can be confusing to the user. The W3C recommends that this tag not be used. We recommend using a server-side 301 redirect instead.