It was never said that all 3 calamities were going to MF on their respective ships. we dont even know Kaido had 3 calamities at that time as you know Drake can still be one of the calamity.We have Kaido on his own ship,Jack on his own ship and the other 2 Calamities on their respective ships.
All guys in Kaido's crew doesn't have df. for example:Scotch was kaido's man and he was only a cyborg.How will Shanks manage to stop all them lol. And since its implied Kaido's crew are DF users they would all just sink in the water and die is that what you're saying happened?
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This is also a reason Kaido was no1 buyer of smile df from Doffy.
Its not that hard to destroy a ship.Pretty sure Kaido was going to Marineford alone as part of his Suicide attempt and Shanks and his entire Crew intercepted him.
Shanks could have used long range attacks and destroyed mast of kaido's ship making that vessel invalid for transportation.
He doesn't have to destroy the ship as whole.