The Jeep Wrangler probably has the highest proportion of after-market modifications of any car marque globally. In almost every country where the vehicle is sold new or used you will find modified examples.
If a 'JK' Wrangler is running on 37" tyres then any crook will spot it instantly as being special. If the vehicle has been built for rock crawling or expedition use you can assume $2K went on tyres. If it had stronger replacement axles these will be instantly recognizable without having to get under the vehicle. $6K+ per axle is a reasonable starting value. My guess is that the crooks were targeting 'Rubicon' models and any modified Wranglers as the parts will be far more valuable than the base models.
In the UK, the current Jeep Wrangler has to have a factory fitted bonnet lock due to UK insurance 'Thatcham' policies. In most other markets the bonnet/hood does not have a lock and can be opened easily from outside the vehicle. This is an artefact from the WW2 Jeep that is extremely practical when the vehicle is used off road but Jeep really could have put some design time into securing the hood for dual purpose street/off road use. Having to open the hood with a key when you are knee deep in mud or water, or in freezing conditions when the lock has frozen isn't practical.