It really comes down to what your needs are, you’re expectations and commute.
I grew up in the general area, primarily PH and yes there were some pretty rough areas. Fortunately or unfortunately, the cost of housing has driven out most of the trouble makers within the city. Living in PH you’ll be within 30 minutes to most of the city.
You’ll be looking at older homes but, there are some amazing lots in the mix. Some are super deep and some really do have some great views.
It’s been a long time since I lived in the area but, I’d consider the near Parkisde just north of the 54. It used to be fairly quiet without too much drama. The potential downside being the schools. You’d be 10 minutes from the base, 15 minutes from downtown, 10 minutes from Eastlake/Otay Ranch and 20 minutes from Mission Valley.
As far as security, I never had any real problems. Just pay attention to what’s going on around you. That’s just a good practice regardless of where you live.