The days of pulling off the highway and camping alone anywhere in Baja are pretty much over. For 20 years, I did just that regularly without a care, but no more. There is just too much drug-related crime these days..much of which is meth. Think safety in numbers when choosing a dry camp.if you don't want to use one of the many RV parks.
But not to lose hope, you will find many secure places with a little investigation. For just one example, The Bay of Conception south of Mulege does offer many dry-camp opportunities right on the beach. All the north end beaches are relatively safe and are very popular with dry campers. I would not recommend the deserted southern end where there has been a history of petty theft. Also, I would not recommend being the only one at a camp that is highly visible from the roadways.
Listen to those hairs on your neck.
As in all decisions about security, forewarned in forearmed.