I don't know, maybe this has already been revealed, but I couldnt find anything except complaints about it being bugged when the game was new, so I figured I'd reveal my findings.
Math and shit ahead...
Based on looking at the leaderboards and scores on youtube, as well as a couple of my own experiments, I believe what I have found is correct, but might be incomplete for playthroughs longer than 1 hour.
Basically, the time-bonus is calculated based on time as well as your total non-timed points. More specifically, the time you play a mission in yields you a percentage which is then used on the non-timed points to calculate the bonus.
So a perfect SA playthrough (which gives you 100,000 non-timed points) with 50% yielded from your time gives you a time bonus of 50,000 points and a total of 150,000 points for the entire mission.
The percentages are:
110% for 0 minutes (210,000 points in total with SA)
70% for 5 minutes (170,000 points in total with SA)
60% for 15 minutes (160,000 points in total with SA)
50% for 60 minutes. (150,000 points in total with SA)
The percentages for any other time are calculated as linear interpolations between these points, so for instance a playthrough of 2 minutes 30 seconds gives you a halfway point of 90%, while 30 minutes is a third the way from 60% to 50% and thus gives you approximately 56.67% as a bonus.
This gives you a theoretical upper cap of 210,000 points (which people got when the scoring was bugged), while most players who do SA will rarely go under 150,000 points (1 hour).
It also means that for certain times, someone who doesn't get SA can still beat someone who gets SA,
For instance, if you get caught on camera and don't delete the footage you can beat an SA score that was done in 1 hour if you do yours quicker than 2 minutes 48 seconds.
But if the SA score you want to beat while not deleting tapes is done in 5 minutes (for instance) you can't defeat it, because you can get at most 168,000 points, while your opponent has 170,000 points.
There might be another data point after 60 minutes (I haven't done the experiment yet),, but it looks like it just continues in the same way as between 15 and 60, so hypothetically you might be able to get a negative time bonus (uness IO have put in another data point, or a cap at 0 %).
I dont know if this was of interest to anyone, or if perhaps it is already common knowledge, but in case it isn't common knowledge I thought I'd share.
Added by Edit:
This also means if you want to break 200,000 points (with SA) it puts you one fourth the way from 110% to 70%, which corresponds to 1 minute 15 seconds.