The n48-52 magnets I use* seem to be fine on the bases with a little bit of superglue control gel (one of my friends uses several in his Knight bases), I suspect you'd have to be very careful with putting them if the model is already on the base and avoid putting them in a box or whatever for a while (as I've noticed the bases seem to get a bit of an uneven white coating, which i suspect is the superglue outgassing, when i put them into a box soon after fitting the magnets (it normally seems to wipe off the bare plastic, I think it's basically doing what the police do for some fingerprints where they use superglue fumes to get the prints to show).
For most miniatures I've found a single 3mmx2mm disc magnet seems to work well with "paper metal" and extremely well with actual metal.
One tip I always give in regards to using magnets, is make sure you stick to the same orientation on them
Most obviously if you're doing interchangeable weapons, but also bases, that way you can use the magnets to stack spare bases and use any base to hold the magnets you're using for weapons (and to help make sure the magnet is flush in the weapon/option which is very handy for Tau drones**).
IIRC a couple of my friends tried things like metal washers and coins in the bases for metal miniatures, which can help with counterbalance, but you usually can't put enough weight into the base, although it can certainly help a bit.
*Spider Magnets on Ebay are my normal supplier as they have a good range, clearly marked and usually ship same/next working day from inside the UK.
**Most of my drones are magnetised as it makes it easier to store/transport them and the flying base pegs are so brittle they often break if you know the drone over anyway.