Level one suspicions are counted for suspicions but not for the score (it starts from level 2) because in some FMs they are impossible to avoid, like you spawn into them or sound through a bottleneck goes through the walls and the player has no indication it happened, and the score is for ghosting, so it's following the ghosting rules, the AI has no idea a person is there. But if you want to be hardcore, you can attempt zero suspicions as well, like super ghosting.
As for searches, the issue is searches last a long time and cascade, so the first version had scores going into the 100s or 1000s which was absurd (we thought). So we took out cascades and level downs, just counting the highest level in a time frame (the peak in a mountain range), and we counted the duration of a search instead of adding to the score every second he reacquires, which again blows up the score. Basically it packages alert situations into roughly contiguous units in a time frame. An AI has to completely level down and wait a bit before a new search is counted as a second, independent search. A string of 20 searches in microseconds of each other, quick level downs and level ups, are considered part of the same search. (Grayman did most of this with me helping with little things like the gui. But we were discussing the system together.)
It took a lot of tweaking to get it to its current state, but the score explosions were kind of ridiculous, that one minor incident could be a difference of like 80 or 200 in the score.
So if you're independently counting alerts, you could either take the sourcecode algorithm the stealth score uses directly, or just use different terms so it's understood it's different than the score.
All that aside, I'd be interested to see a cleaner gui set up with a little optional light that's off, green, yellow, and red by the current alert. For a ghoster, that light is the measure of a bust, without needing to add it up. But you could add it up with that too.