When you're trying to shoot your way out of a secured facility with unsilenced fire, the only time it's safe to reload is when you don't have to.
It's seriously 3 seconds. You likely can even keep moving while reloading since you're putting away stuff and not just dropping it as a free action. You take out 6 guys, reload, and continue in 6 seconds. If you have 2 minutes to get out, you've only used up 5% of your time worst case. If you didn't have to reload, you're only saved 3 seconds or 2.5%. If you really can't stop to reload, maybe you should just be using one firearm at a time since it's not security guards that's your weakness but a 2 second window.
I guess if guards were coming in 2 at a time every 3 seconds and you had to defeat them in a new battle each time, reloading might matter. But in that case, the guards really ought to wait 3 seconds and come in a group of 4 and take you out. They aren't in a martial arts film with guns.
Edit- There's also the fact that the vast majority of games once combat is done, no one keeps a careful track of time. You can just say "I reload" as you go out of combat time. If you are keeping in combat time, the 2 minute countdown is seriously 40 combat turns and that's a huge pain in the ass to keep track. Record keeping alone (asking people what they're going to do on their action and them saying "I hold" and keeping track if it's pass 25 or 27) is going to cost you a fair amount of real life time for what basically is "I want to make sure on the off chance a 2 second longer reload will kill your character."