You yourself provide the basic answer in your third sentence.
I read the two articles you provide and find them to be basically a retstatement of just about every other story on the topic. Slow news day or week and the reporter wanted something to write.
Having visited Central America repeatedly the last 2 decades I can only say , like you did, that if you want to go looking for trouble you can find it. I even make San Pedro Sula and Tegucigalpa ,San Jose, Panama City, Guatemala City,Reynosa,Matamoros et al overnight hotel stops and I remain comfortably i n my room .
Like any large cities,anywhere, there is the caveat that you must be alert for your safety and stay away from neighbourhoods of questionable repute , be ever vigilant for street muggings, and avoid drugs and related activities.These were points of advice long before this drug war business blew up.Simply riding through parts of a city will provide some sense of how the security situation might be- is it upscale businesses , well kept residential or slummy and garbage strewn ?
Stay off the streets walking or riding after dark and you should really have no problems.
Come and enjoy your visit.