There was actually never any sort of restriction on using real guns or not. It was just up to the producers most of the time. Some played it safe like Spiderman TAS (just lasers) while others took it a little darker like Batman TAS(mostly guns). Both were on Fox at the same time.
Once these shows started running on Cable, they could show whatever they wanted. The majority of the time producers played it safe. By the time Superman TAS came around, it was airing on The WB, a cable channel. If you go back and watch Superman and New Batman, they deal with death and murder a WHOLE lot. There's tons of overt sexual references. Why? Bruce Timm and Paul Dini weren't trying to make a kids cartoon. They set out to make a cape show for general audiences. It worked amazingly well. The animation was WAY better than it had any right to be too. You know the same animation studio that did Akira did Superman TAS? It really shows with some of the original character design as well as the lighting and shadowplay.