If you want to introduce a note of (unwelcome) realism:
Wooden ships don't sink (usually)
Up until the development of ironclads, it was rare for a ship to be sunk in combat. Partly this was because the opposition didn't want to sink them, they wanted to capture them, but mostly its because wood, unlike steel, floats in water. If you need to know why this matters have a look at how ships work. In essence, if the average density of the ship, the stuff on and in it (including air/water) is less than the density of water (about \$1027\text{ kg/m}^3\$ for sea water or \$1000\text{ kg/m}^3\$ for fresh water although they both vary with temperature and salinity - not all seas have the same salt content) it floats, otherwise it sinks.
Putting holes in a ship below the waterline allows the water (at the density above) to displace air (about \$1.3\text{ kg/m}^3\$ which will increase the density of the ship. This will cause it to reach neutral buoyancy with less ship above the water and more ship below the water. At some point, the waves on the sea start going over the ship rather than around the ship so the water starts getting in at the top rather than the bottom - at that point the transition from 'sinking' to 'sunk' happens rather quickly. When this happens depends on the design of the ship, the size of the waves and if its settling evenly or with one end down and the other end up.
Many, many wooden ships were 'wrecked' but that is different from being 'sunk'. A shipwreck happens when the ship strikes something - a reef, the shore etc. and becomes stuck. The waves then twist and buckle the ship until it suffers structural failure and breaks apart. This can happen to steel ships as easily as wooden ones although modern navigation aids and charts mean this is today a very rare occurrence - Costa Concordia springs to mind.
In combat, the biggest threat to a wooden ship was fire - either caused by enemy incendiary attack or by accidents with their own fires. An out of control fire could easily burn a ship to the waterline after which the hull would sink because see above.
Ram armed galleys could sink each other but this worked because of their relatively light construction and the low freeboard that the oars made necessary. Even so, sinking was a secondary objective - you rammed the enemy to allow your troops to board and capture the ship while their troops had to deal with the consequences of being rammed - like being dead, trapped under debris or trying to stop their ship from sinking.
A fire attack is going to be more realistic than knocking holes in the bottom - unless its a really big hole - like that from a Passwall spell. Or a really small ship.
Of course, your idea is way more fun - so do what @BenBarden says.
What the crew can do
All ships leak and therefore they have pumps designed to remove the water quicker than it can get in - usually a lot quicker because the pumps require manpower and you don't want to have to work the pumps 24/7. Of course, if someone has knocked holes in the bottom of your ship, you will do it 24/7 until you fix the holes.
You can also change the average density of your ship by throwing heavy stuff overboard - anything made of metal is really, really dense, for example, steel is 8 times denser than water. A cargo ship can offload its cargo and a warship can get rid of its weapons.
The other thing the crew will do is plug the holes - to this day navies employ ship's carpenters for exactly this purpose. Even though ships are built from steel by boilermakers they are patched at sea with timber by carpenters because timber is quicker and easier to work with than steel - a vital consideration when people are shooting at you.