I've been thinkin about this for a long time and since I didn't find anything similar I decided to shar this idea here.

Better Bots Mod gives players a option to allow bots mask up and be on guard if they hear an loud noise during stealth without triggering the alarm, the problem here is that if you manage to keep your game in stealth after a bot masking up it'll keep following you anywhere you go, most of the times when that happens civies, cams and guards get's alerted by them and send stealth to space, and the worst is that you can't give them an order to stand still.

This is where my request kicks in, it would be really helpfull to have an option or maybe a mod to combine with better bots so we could give orders to AI while in stealth.

Yes. you can. its called [Z]. forces the bot to stay where they are.

this action only works in loud, I'm looking for a mod that allows you to give orders to bots in stealth

I think you're looking for Keepers, you can give commands to bots while in stealth. Such as telling them to go somewhere, stay still, answer pagers, and you can also combine it with GoonMod's custom waypoints so you can make your NPCs go wherever you want them to. And there's also MonKeepers, which makes bot able to collect loot bags like you and transport them to a drop point.

Keepers
Custom waypoints
Monkeepers

I use all of those combined with Better Bots, and they seem to all work pretty well together.