If you have really bad karma or live in a really high-theft area, take your saddle and pedals with you. Nothing will stop a determined thief---and anyone who would steal your pedals ... that's just hard to fathom. Why did the guy have the necessary tools? Not a random thief, but obviously not much of a bike thief ... maybe you made some enemies?

But yeah, any lock can be defeated, any chain cut. If someone is out to get you, or out to get bikes and gets malicious when he can't steal yours ... don't leave anything removable on the bike. Of course, if the guy carries pedal wrenches and Allen wrenches, he could steal your derailleurs and brakes, too .... really, it doesn't end. If he brings the tools, he could steal your headset and fork, how could you lock that?

If you really don't feel secure, throw the pedals and seat in a plastic bag and take them with you.

Maybe it was a one-off by a malicious, petty person who will never again cross your path ... but locking up your bike in any public area is always a gamble. You have to decide what you are willing to risk.