They don't store over restart, they don't store when garaging the vehicle and unless the server goes down unexpectedly i do not think you can be comped for then Y menu items store if they are legal.
Nah I don't think you can be comped. As far as I know the RP way to think about it is -
The garage owner is a model citizen and when he repairs and puts your toolkit in your car he will more than likely notice any illegal items in the car (Y or otherwise) so he will confiscate these and hand them into the police.
Edit: Or he keeps them for himself cause he's a thieving little ****
@Lecter legal items used to stay in cars over resets/storage of the vehicle, whereas illegal things didn't. However, this was recently changed due to people storing trucks full of legal substances, and pulling them out nearer the traders for example (teleporting the items in order to make quicker money). I believe anyway.