No reason why it should. I have both my chartplotter aerial (navman 5500 and normal GPS (magellan) sited permanently inside my GRP wheelhouse to avoid damage to them and only occasionally have a slight problem when totally surrounded by lots of very tall boats in a marina.
Should be no problem. We keep our handheld (Garmin 12) lying on one of the quarter-berths, with no extra aerial, and have a repeater fitted in the cockpit. We've also fitted a cigarette-lighter socket so that the GPS doesn't eat too many batteries. It all works fine.
I have just fiited a chartplotter under the sprayhood. I was worried about the struts getting in the way of the heavens but it works absolutely fine and is far better IMHO than fittings on the pushpit which are so exposed to the elements and getting knocked.