I use my Honda PCX150 for commuting and have a top box. Ok, it's not the coolest thing but it gets me to work on time with a big grin on my face. Recently I came back to my scoot and it looked like someone had tried to remove the whole top box frame. I guess so they could steal the topbox. Is there any way to stop this? Ultimately it's only held on with a few bolts.

You can get security bolts which would slow down a thief considerably by making the nut inaccessible.

Someone with simple hand tools will always be able to remove a top box or get into it fairly quickly but that's true of most car boots too.

If the top box is empty you could consider leaving it unlocked so they can see inside. There again they may have been trying to nick the box and rack itself as these make good money on roadside sales at the weekend Khlong Thom market in Bangkok so security bolts are probably the best plan.

See here an example of some security bolts;

Just to add to what has already been said, there are a wide range of security bolts (and nuts) available that you could use. A good resource you may be interested in taking a look at is the Security Fasteners website www.securityfasteners.net, which has a lot of information on the different types available. Its important to bare in mind just how secure you will need to make your top box. For example, you could use a high security wave bolt, but the premium, high security nature of this fastener means that it does come at a higher price. You may be okay with something like a Pin TX or a Pin Hex as a deterrent to any potential thief, but this is your judgement call.