There still is a significant difference. The Hiroshima and Nagasaki bombings were done by the US military and with President Truman's orders. While each bombing killed many people, a government (in this case, the US government) had completely control over A) when those killings were to occur and B) why they were to occur.
In the Philippines, it is very likely that someone intends to exploit these relaxed laws. This does not bring comfort, when at any point, someone who may not particularly like you decides to kill you.
I am actually impressed that "only" 3500
have been killed so far. The police say they are investigating 2233 people killed by vigilantes whether they were actually drug related, but I doubt they'll be able to fully investigate all of them.
The time is perfect in the Philippines right now, if you have someone you need to dispose of, without raising suspicion.
But maybe both of us should be glad we don't live in the Philippines, because I certainly would not want to be there right now.