I've seen a lot of casual antenna-performance comparisons on the Internet through the years, and the general results were that, inch-for-antenna-inch, the magnet-mounted antennas were as effective as those permanently mounted in a hole. The key seems to be the antenna length and where it is placed on the car, the best generally being in the middle of the roof. This is one recent example I ran into:
"Magnetic mounts (good quality ones anyway) have little significance on an antenna's performance, just as the Larsen PDF illustrates: a tiny loss of 0.2 dB with a magnetic antenna vs a permanently mounted antenna. That paper also states the minimum amount of effective ground plane needed for several frequencies; but, of course, CB @ 27MHz will require much more ground plane than 150MHz will, making it all the more detrimental to the signal pattern to have it on the fender of the vehicle instead of the roof. I've seen it many times in the real world too, where I could clearly hear a buddy of mine who has a magnetic roof-mounted antenna, but signals from others who had various non-roof-mounted antennas (most being non-magnetic) were not even detectable."
Correct. When comparing like for like antennas, mounted in the center of the roof of a vehicle, there is a 0.2dB loss for the magnetic mount. It's highly unlikely anyone is going to hear that 0.2dB difference.
All things being equal, mounting the same antenna on a mag mount versus a permanent mount isn't going to amount to much.
However, there's other things you need to consider.
There is a difference between a capacitively coupled ground plane and a real ground plane. That's where the 0.2dB comes in.
But if your antenna is not working well, you can have stray RF radiating off the outer shield of the coax on your magnetic mount antenna. That can be a problem.
Then you have to get the coaxial cable inside the vehicle. Sure, run it through a door, window, etc. However, running coax through the door risks pinching the cable. Pinching the coax changes it's characteristic impedance. Now you've added to that 0.2dB of loss.
Pinching the cable/abrasion between the door/body risks damaging the cable jacket. Now you risk getting moisture inside, which will corrode the copper. Now your coaxial cable is compromised.
And running through the weather stripping risks letting water inside your car.
Leaving a window cracked, especially the rear slider window on a truck, creates an entry point for anyone that wants what's inside your vehicle.
And then you have vehicles that magnets won't stick to. My F350 is aluminum, so even if I wanted to do a mag mount, it's not going to stick.
And then there's coaxial cable routing. Having it run across the roof of the vehicle from the antenna to the door can result in the cable flapping against the body. The noise can be annoying. The damage to the paint can be annoying.
And then you have to route the cable to the radio. Personally I don't like any wiring showing in my installs. I don't want a cable draped in through the window and across the back seat to a radio. That sort of install just doesn't sit well with me.
And those with newer cars don't want to risk paint damage from mag mounts. Some don't care about the looks of their vehicles, some do.
I have no problem with others choosing magnet mount antennas if that's what their skill level allows. But they do have their drawbacks. It's a compromise. Some are willing to accept the compromise.
It comes down to magnet mounts being the quick/easy compromise antennas for consumers. They don't require any installation skills, so they are attractive solutions to some users. Nothing wrong with that.
But they don't really compare to a properly installed/designed/tuned antenna.