i have a similar story to blueram... i've been using a couple on several acrylic tanks for many years (and still do). i used to just keep it in the tank on the rear side for convenient access and use. anyways, at a party at our house, a couple of young kids discovered the magnet and decided they wanted to help clean the tank while i was outside bbq'ing. argh! yup, gravel and acrylic definitely do not mix. now, i keep the thing locked under the cabinet. these were on smaller tanks (20, 40, and 60 gal) which are comparatively low cost, so i have no reservations using them on those. a 5k gal tank is a much different story.
basically, you just have to be careful when you initially 'connect' the two pieces making sure you haven't caught anything hard between them and when are you scrubbing near substrate. the same thing would hold true using any algae pad-type scrubber for acrylics tanks, whether it's handled or not.
-snafu