In layman's terms, just don't be the dumbass who makes it too easy not to steal. Don't leave your deck sitting out at your LGS. Keep it boxed up and with you at all times. Myabe the store owner will let you stash it behind the register or something..a safe spot. If you carry your stuff in a bookbag, don't leave your bookbag sitting around. if you live in an apartment complex or a sketchy residential neighborhood, don't leave it in your car overnight--take inside with you. If you DO leave it in your car, be sure to LOCK IT, turn on the alarm, don't just throw it on the front seat where anyone can look in and see it.
Now, I don't know you at all, so please don't take this the wrong way, but here's the most important one. (It's still 100% common sense though.) Don't be the guy who can't stop talking about his awesome super-valuable masterpiece cards. The type who enjoys having a crowd of younger players standing around, gobsmacked, looking at your amazing cards. Thieves are thieves because, among other things, they covet nice things that you have. If you are the type of person who shows up and just tries to endlessly impress everyone with your latest super-pimp cards, guess what, IF there is a thief in your midst, you just got his attention. You just became his mission. They are patiently waiting for the first opportunity to steal them. Frankly, you did it to yourself in that case.
Another one, also obvious, don't associate (or form a playgroup) with dirtbags. Seriously...find a playgroup (and/or an LGS) that isn't the most sketchy one in town. Seems like every city has at least one. Avoid it.
Honestly, if it were ME, I'd sell them and just replace them with regular versions. You still get to play the cards you love, you can now afford to acquire MANY MORE cards to play with, they're (far, far) less of a liabiilty, and honestly, Masterpieces are just kinda ugly to me. (It's like FTV foils. Eww?) To each his own..
Good luck with it!