Sonic Frontiers.

-Astro Boy Omega Factor
-Kirby Super Star
-Kirby's Return to Dreamland
-Tokimeki Memorial
-Rocket Knight Adventures
-Sparkster (SNES)
-Family Guy The Video Game

Viewtiful Joe

No More Heroes 1 and 2

Both Freedom Planet games

gunstar super heroes has levels that pay homage to thunderblade, afterburner, etc

also cybernator/assault suits valken

The Wonderful 101, Bayonetta 3 (I think 1 has one too, haven't played it myself), Kingdom Hearts 2 and 3 (1 is a bit meandering and lacks the feel of a shmup), and Super Smash Bros Ultimate becomes a shmup during the Classic Mode credits.

Does the credit minigame in Smash Ultimate count?

Shadows of the Damned, Pac-Man World/World Re-Pac, Kirby's Adventure/Nightmare in Dreamland, Crash Bandicoot: Warped, Bloodstained: Curse of the Moon 2, and Spy Fox in Dry Cereal.

jade empire

Kirby & the Amazing Mirror, just before the end.
Super Mario Land has some plane stages.
WarioWare, Inc.: Mega Microgames! has a boss stage that is played like a shoot'em up.
Metal Slug 3, when you are in outer space in the Final Stage.

Hope all of these count...

Thanks for all these suggestions everybody!

https://backloggd.com/u/lpslucasps/list/otherwise-normal-platformers-that-have-a-shmup-level-for-some-reason/