My power armor disappeared from Sanctuary which had settlers and turrents/guards... etc..

How?

Can even guarded armor get stolen? How should I store it if I find a replacement?

AFAIK settlers might just enter the Power Armor and do.. things with it? To prevent this, remove the Fusion Core when leaving the Power Armor anywhere behind.

You got power armor jacked. Next time, take the fusion cell out of the power armor when your done with it. It's kinda like going to the grocery store, shutting the engine off, but leaving the car unlocked with the keys in the ignition.

Dont feel too bad its happened to me too. I even had 3 suits of armor standing next to each other in Sanctuary and 2 of them got jacked. We live and learn.

keep it at your sanctuary so it doesn't get stolen. I keep mine at the first sanctuary and keep spare parts in a box next to the building station and I haven't had anything stolen ever.

I did take the core out

Ouch. Not sure what happened then. Maybe it bugged out and reset somewhere? I've read that other people have things vanish on them. Luckily it hasnt happened to me yet. My luck must be 10.