Chris,
One factor is related to the comment that Eric made about the fraught time one can have whilst drying out. The bilge keels, whether moulded in (Ivory Gull) or bolted-on steel plates (Golden Hind), are not as strong, and as strongly attached, as either the central ballast keel or twin ballast keels need to be. I remember an occasion when I miscalculated the tide height by a few centimetres, and spent an anxious couple of hours at the bottom of the tide, swaying to and fro with the very small waves, no more than ripples really. The central keel was firmly aground and each bilge keel was slamming down onto the hard sand (I try to dry out at half tide, when possible, so that it takes the least time from first touch to being settled down firmly). This doesn't happen in the same way with twin keels, and anyway, if they're not up to thumping down onto a hard sand bottom, there's something seriously unsatisfactory with the construction of the boat.
The performance disadvantage is chiefly due to having much more surface area and therefore skin friction than strictly necessary; but possibly also because triple keels are less hydrodynamically effective than twin keels, though my reasoning is a bit woolly, and I wouldn't want to defend that thought against rigorous examination. I did find with Ivory Gull that there was much more leeway than I thought there ought to be.
Twin keels can be very efficient, if properly designed, but I don't think triple keels ever can be. Examples of well designed twin keeled boats are the Sadlers (eg my Sadler 25 Lliutro) and Hunters (eg my Hunter Duette Weaverbird), and the newer RM890, but I can't think of a triple keeled boat that sails well to windward.