The Thousand Isles are extremely advanced when it comes to Naval Warfare and far less advanced in land battles and sieges. The nature of the islands and the terrain make it difficult for opposing powers to field or transport large armies or conduct drawn out sieges. Also many of the interiors of the islands are wild and mountainous, ideal for guerilla warfare. Generally the wars are settled at sea, since most states are so reliant on sea trade, destroying their navy and embargoing their ports is generally sufficient to force a favorable settlement. This also plays well with the goals of most of the merchant houses that are often pulling the strings of the various rulers, they are generally less interested in territorial acquisition as they are dominance of the sea and trade lanes.
The few times where the struggle cannot be settled at sea, the armies of the major states have struggled to achieve offensive goals. Several times in recent history inferior forces have been able to frustrate invasions of markedly superior forces via fortifications, defense in depth and guerilla warfare tactics (Southward Isles, The Garden Isles, Invasion of Ende). At this point in history the major powers have become more or less convinced that such land actions are somewhat futile and the established land warfare doctrine is that no island can truly permanently conquer or subdue another via invasion unless allied with a native faction.
The current naval doctrine of most islands favors large fleets of galleys. Haven especially is wedded to this, and has invested in a ridiculously large and powerful galley fleet. These fleets tend to be powerful short range strike forces, especially in the calm inner seas, and have the advantage of not being as influenced by vagrancies of wind. They are fast for short sprints and powerful in combat, especially compared to their relatively low cost. However they struggle in force projection outside of their preferred operating theatre, deepwater actions in the Reaches for instance or in the Etish Sea. They are also in danger of becoming anachronisms as the struggle to mount the larger cannon.
To compensate for the disadvantages of galleys, The Republic of Haven and most other states maintain relatively small deepwater fleets of light, fast pirate hunters and also utilize privateers and impressed merchantmen in times of war. The merchants on the other hand have trended toward larger and larger Galleon to fend off pirates by shere size, or lighter faster and heavily built Fluyt. Merchants also often travel in convoy All these solutions are generally not sufficient to keep the pirates under control, so occasionally the major powers band together and launch a crusade on piracy to sweep the nests clean. These crusades are generally successful at suppressing piracy for a few years, but the pirates always come back.
The notable exception to the prevailing naval doctrine is Etmarch. Separated from the rest of the Inner Archipelago by the large and stormy Etish Sea, Etmarch has focused it’s naval strategy on dominating that body of water and thus preventing invasion. Thus Etmarch has the best deepwater navy in the Isles. The Etish Islands however are generally not much affected by piracy however and strategically needs to keep that navy close to home, so the fleet rarely sees action and doesn't really affect the piracy equation much. It is interesting to note that when the Entmarch fleet was fully deployed against the Havenites ten years ago in the War of Antillian Succession, the deepwater ships acquitted themselves quite well even outside of their preferred operating theatre .