Backtracking a minute here.
(what was he conveying when he shook his head after looking through two doors in this room?)

There wasn't anything of importance in the hallway. Feel free to explore it if you want, it's just that the character of the detective didn't see anything of interest, and was letting yall know that there wasn't anything there.

"The secret doorway is here with the corpses. We came through into this room but not through any regular doors. If we are trying to find the boss, we should find the secret door"

Huh. I entirely missed the fact that we used a secret door.
Would we be able to just remember where it was?

Quote from Elgoblino10986 >>

The two men lead you outside of the room, chuckling like vultures when the boss orders the thug inside. They exit the elaborate room, going up the stairs into the main warehouse. They go to the upper side of the warehouse, walking into a kitchen, with scents of broth, humid air, and lanterns hanging on the cieling, where a kobold in chefs clothing is working on a meal, standing on a stool to reach the pot. "You better not mess up my order," one of the goons says offhandedly, yet somehow filled with malevolence, causing the kobold to flinch. The other one opens a secret door, leading to a dark, lightless room filled with coffins, with a cloaked figure sitting on a crate. "Sup, corpse," the other goon greets it, but it does not respond. Peyton and Apa feel a sense of unease from the figure but the 2 goons have already opened the final doors. "Take these, holler if you need help," the first goons hands you two clubs, a cruel smirk on his face. 

 Here is the post with the secret door

Oh thanks.

The detective goes to the door where you entered this room for the first time. He looks around for the secret door, making a perception check: 9

Apa follows suit 

Perc: 7

You immediately fond the secret door from memory. "Oh, thank you," the detective says. Apa, you are immediately hit with the hot air from the kitchen. The kobold stands at the opposite end of the room, still looking pretty scared.

Uhm, why would it 'still' be scared? from what?

When the 2 goons walked in it was scared of them, and it's scared of you guys now, maybe due to the disguises, maybe not.

Apa walks in and nods to the Kobold "All good here?"

Uhm, Apa isn't in a disguise.
Isn't the general idea that the detective and Sirrus are playing guards, and like I don't know, bringing the two of you somewhere?
Not sure. It seems like we just put on the disguises and left without all that much of a plan. Or were we just trying to get out of here?

The kobold stares up at you in fear, even as you ask those words. He tries to speak, but cannot get any words out, opting to nod his head.

Sirrus gives him a quick nod.
"You got any spare meat lying around? I'm starving. I swear we never get enough blasted food around here."

The kobold nods his head and points to a stew with chunks of cooked meat in them. The detective whispers to you three. "It'd be best if we keep a move on. We don't know if the kobold knows we are fakes, or if it will report us to the boss."

(BTW sirrus the detectives main plan is to sneak to Geffanos office and arrest him, it's also good to try to find evidence and a way to make a quick escape)

my understanding was the "goons" and not disguised folks were just walking to the boss to report back while "Sirrus" is still questioning the prisoner.

Right, got it.

Sirrus nods his head in appreciation and grabs a hunk of meat to gnaw at.

I suppose at this point we will just keep going until we come across something.
We should however move at a slow pace for increased perception.

Apa nods to the Kobold and quickly says as she walks by "Say anyone else give you a hard time, I will clonk them for you...Your food is good" 

Peyton nods her head in agreement. Kindness should be repaid with kindness.