This guide is not meant to help you find every secret within a map, I can't do that with a procedural generated game.

This guide is more to help newer players or serve as a reference.

Secrets come in 4 varieties;

Damaged walls; walls that have holes in them

hidden doors; doors that look like walls but have stretched textures

power boxes; small boxes attached to walls

switches; buttons or destroy able switches that unlock doors/force fields

While there are only 2 mission types right now (collect and meltdown) it is worth mentioning that when playing meltdown your secrets could spawn in compartments/rooms that only open after activating the self-destruct sequence and 1-minute timer, but it doesn't always happen.
I end up prioritizing collect missions and avoiding meltdown for that reason.

FLARE FLARE FLARE ROCK AND STONE FLARE FLARE
throw them flares like you're shooting bugs in mines

Damaged Walls are easily visible once you get used to looking for them. The holes in the wall are transparent and let you see thru to the other side.

you can see a green something through the holes in the wall in the second pic ^

Hidden Doors are the worst secret as they don't really have a good identifier like the damage walls. The thing to look for with hidden doors is stretched textures

Power boxes like to be in dark places and are quite easy to miss

Switches are the easiest secret to find and sometimes don't even unlock secrets, they glow green to help find them, but still check your corners and everything!