Worst possible outcome involves Crusaders stealing the holy meteor, but they never make it home. During the return trip, they are attacked by Barbary Pirates and their ship sinks along with the holy meteor.
They'd have to be time-travelling Barbary Pirates.
But yes, abducting the Black Stone by sea opens the possibility of it sinking, which would cause... problems.
I still question the material feasibility of the whole thing by Crusader raiders anyway. It's an extreme feat for them logistically. The attacking force must be necessarily small and probably undersupplied, operating in an extremely hostile human and natural environment, with unfamiliar winds in the Red Sea, a situation on land where they preferred combat style and equipment don't work well, no knowledge of the terrain, fighting against fiercely motivated locals who know the area, are well-adjusted to fight there, and enjoy higher mobility. The defenders of Mecca here would also be better supplied and almost certainly more numerous. And the terrain around there is unforgiving. Seriously rugged, with little or no water, unless you know where to look for it, which the defenders do and the attackers do not, and otherwise difficult for the invading party in many ways.
The odds are stacked horribly against the Crusaders at every point. Which probably helps explaining why such action was never attempted by any Christian power at any point in time.
(I concede that Mecca is not very far from the sea, so the stay in the desert is going to be short enough before getting there that the supplies could be physically carried. But then, Mecca is going to be defended, and there is no way the Crusaders can sustain a siege).