Some fun stuff. You'd generally want to hit light targets with lighter weapons e.g. machine guns, CIWS, autocannons, AGLs, AA guns, etc.
For IRL example on why, see the Chinese communist campaign on Hainan Island. Basically, the CCP screamed Leeroy Jenkins and rushed the KMT with a fleet of wooden transport fleets. The KMT had a proper navy with actual military vessels. When they fired, the armor piercing shells tended to go straight through the wooden vessels and detonate beyond, without damaging the ship. In addition some of the ships were so low in the water the naval guns were unable to depress low enough to hit them. The KMT then attempted to board and capture the wooden ships, upon which they ironically became outgunned because the communists jury-rigged artillery pieces to fire shells at point blank range. End result KMT lost their flagship and the communists somehow lost no boats.
TL;DR the KMT's navy got defeated by a fleet of literal junks because lightly armored vehicles hold up surprisingly well against dedicated armor piercing weaponry. The whole Hainan island episode is actually a hilarious sequence of inadvertant actions by both sides.