Some of the automatic transmissions that I've taken apart have magnets on the sump plate. I'd think that as long as it is upstream from the filter, it isn't going to travel anywhere. On the downstream side of the filter medium, I'd be a little worried.
At least a few of us added magnets to the outside of our stock filters:
http://986forum.com/forums/general-discussions/60715-my-take-magnetic-oil-filter-housing.html
I've had mine on for one oil change and noticed just a trace of dark slime attracted by the magnets.
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