Okay. So again, not sure why having to have your ship still exist after you log out, with the chance of destruction even in a safe place, makes sense. Surely it will happen at some point, you log out, everything is safe, but CIG's code spawns in pirates during the gap between you logging out and the ship despawning.
I use bed logging all the time now, i live in my ships, the only time i have had issues with my ship not being there the next time i log in is if i bed log near somwhwere that is visited by real players.
These days i bed log in the middle of no where or if i have just done something surface side i simply fly to a high altitude and bed log outside atmosphere.
Never had a problem if i do that.
.Its as it should be, leave your ship parked up for someone to find don't expect it to be there when you get back.