If you choose a less popular streaming site, not only will it affect the traffic your music sees, but it can also affect how much the site is willing to pay you in royalties. If they aren't a high traffic streaming service, they won't have a high budget to work with for royalties.
However, if the site has decent traffic but not as many artists, you can hit a sweet spot with the royalties they will offer. Given that they have a higher budget and less people to pay, you can really clean up.
Getting your music in a Spotify or Apple Music playlist could be harder than getting it in one on Deezer or a less popular streaming site, but in the end you'd make more money off the song people there's a heavier listener base.
Liken it to getting shelf space at a Target or Wal-Mart vs. a Mom and Pop shop.