I went back with another character (way more than 30 days since the last visit) to check if the bodies disappeared and they were there.
I know that Fort Dawnguard has storage problems even if you side with them, but, once there is no one there alive, does it become safe for storage?
The same question applies to Volkihar Castle if you side with the Dawnguard.
tl;dr: After you kill the opposite faction does their fort/castle become safe for storage? .
Regards.