Nowhere is safe, some places are just safer than others. I would definitely purchase in these areas. I think there will be more appeal in these areas soon because of the proximities to downtown and has low prices for SFHs.
If you’re familiar with Diego (Daygo), the areas of Golden Hill / South Park, North Park, City Heights, Clairemont (lived there, best part of SD IMO), Linda Vista (Little Vietnam), were undesirable to moderately desireable during the years you mentioned due to crime. They are great areas these days, Tavara Ridge in Clairemont had recent sells of $1.5M & $1.68M for that bomb ass model!
A month ago I went to a function at Morse High in VP, Adam Jones the MLB player was there, comfy with his Lambo Aventador ($400k msrp). I departed west on Skyline Dr. and showed my daughter the amazing bay and downtown views from the hills of VP. It dawned on me, the price for view homes in VP are 50 – 75 % lower than Golden Hills and northern SD neighborhoods with comparable views.
I just mapped the downtown commute from a friend’s address in Paradise Hills to Petco Park, came up as a 15 minute drive. On friend’s street, there is a new KB Homes development starting at $650k.