[Pursuivant]

Can the zombies float or walk along the sea bottom?

If so, you've gone from railroading the PCs to giving them the choice between the devil and the deep blue sea.

Let the merc's plan to scuttle the ship succeed (they hole the ship with gunfire or set a time delay explosive charge on the hull) but also prove to be a very bad idea. Zombies go down with the ship, only to reappear clinging to the merc's submersible and/or PC's boat. Plenty of opportunities for jump scares and close quarters combat, especially if the zombies have the ability to cling to the underside of the hull undetected or have the ability to punch or gnaw through boat hulls.

The players will bitterly regret having not just dealt with the zombies aboard the ship when they had the mercs as potential allies, better equipment, more ammo, and a more favorable battlefield.

If the zombies can walk along the bottom, they will inevitably be drawn towards land. The PCs either have to scramble to get ahead of the zombies to meet them on shore and prevent a full-fledged zombie apocalypse on the mainland or have to fight for their lives when the zombies conveniently show up on the island where they landed their boat.

GM's fiat as to whether you want to provide a handy NPC informant (e.g., someone who just barely escaped zombies who crawled the entire length of the ship's bilge to attack) or illustrative scene (e.g., zombies swimming and clinging to the hull of the mercenary's submersible or otherwise demonstrating their aquatic mobility skills) before you let the PCs escape.

There are also methods of subtly engaging the interest of even the most selfish PCs played by the most apathetic players. What motivates the group? Survival? Greed? Power? Give the players a nice, big, tempting reason to hop aboard the G&M Express like the (illusory) promise of safety, or wealth or power beyond imagination.

Put a few zombies on the PC's boat; letting them get away clean doesn't fit the genre. Better yet, make the zombies follow the characters. Create some McGuffin which makes the PCs catnip for the living dead, attracting zombies for miles around. Discovering and dealing with this jinx will be an adventure in itself.

In the course of the inevitable combat one of the PCs might be injured - and the only qualified medical care is back on the ship. If some of the PC's shots miss they might hit vital equipment or start a leak which will eventually sink the boat. Since it doesn't appear that any of the PC's is an expert at boat repair, they'll have to turn back to the ship. Meanwhile, make it obvious to the players that the zombies are selectively following and attacking them.

If you add complications in the right way, not only do you give non-combatants something to do during fight scenes (fight fires, plug holes in fuel tanks, bar doors and windows), but you keep the action moving in such a way that the players either don't realize or don't mind the fact that they've just been railroaded.

If none of that appeals, just rework the material you had planned for the ship scene and introduce it later in the campaign in a way which engages the players' interest and forces their characters to behave proactively.