I generally try to find a place under my fairings or in my bags and run a cable lock around the frame (leave it there permanently), then just lock through the pistol if I leave my bike. Not easy on some bikes, really easy on others. I added a box under the fairings on one of my Daytona's in the cockpit, then converted a cowling from fixed into a hinged lid.

Quite often, however, I remind myself to be practical about things. A bike lock or pistol cable lock around a seat frame is quick and easy. I have owned "truck vault" type boxes and have bolted in other pistol safes... I carry relatively cheap pistols - adding a $500 set up to secure a $250 LCP doesn't make a lot of sense. And a lot of safes which could be incorporated into a vehicle really aren't any more secure than a cable or coated chain lock. I saw a demo once where a guy used a crowbar to rip the bolts through the sidewall of a very popular vehicle handgun safe model in a matter of about 2-3min, which is about as fast as I've seen someone with bolt cutters take out a thick cable lock. If someone wants to steal from you, they will. Spending hundreds or thousands of dollars to secure a low cost pistol doesn't make a lot of sense. I'd be pi$$ed about losing any of them, just like I was pi$$ed when someone stole my phone charger and binoculars out of my truck 2yrs ago, but if someone broke into my truck, cut a cable lock or jimmied one of my gunvaults and stole my $800 Sig, I wouldn't put a $500 safe into my truck. I'd put the same cable lock back on it, and let the theft protection of my insurance buy me a new pistol, and put the same $100 cable lock or same $300ish safe back in place.

I'll follow that by specifying - I have NO qualms about what happens with my firearm after it is stolen. If I make reasonable effort to secure the firearm, but a well-equipped thief is able to take it, what happens with it thereafter is not on my conscience. If a thief really wanted my gun, he could ambush me with a gun drawn when I exit my vehicle and demand I hand it over to them... I'm not losing any sleep over what they do with it later - remember, any criminal who hasn't been caught at least once can buy a gun from any licensed firearms seller, with NO registration of any kind in most states. I don't blame objects for the actions of people.