The simple reason is that active scanners are hugely disproprotionate to their counters. As others have already stated, it takes two complex dampeners, leaving you with less HP and reduces your overall effectiveness. Fine, that stops you from being scanned by proto scanners.

But, in order to be effective, you would have to start avoiding team- and squadmates. When everyone is being scanned around you, your profile dampening is going to be useless. You'll have to start flanking, use backroutes and attempt to just be sneaky. You're slower, clunkier and overall less mobile than a scout, who can get the same level of profile dampening with much less effort, and roughly the same amount of HP with your extra modules gimping your suit.

Then you actually go into an engagement with one of those prototype scanner wielding logis. You get stomped because you don't have as much HP. All your effort was wasted, and it's hard enough to beat proto logis using more effective scout suits.

The simple fact of the matter is that proto logis only sacrifice a single equipment slot, no HP and effectiveness at all to practically see everyone on the map at all times, while you use a ton of SP and sacrifice effectiveness just to not be seen by the scanning logi, who stomps you 99% of the time due to the previously mentioned factors.

When you unload a full mag and and they turn aroundmand insta kill you it gets rediculous