A ship is a very expensive investment and an asset whose repairs, upkeep, provisioning infrastructure, and wages are generally high. Thalassocracies in general were about power projection and empire, either through trade or tribute, and to accomplish this required significant investment from the state. Also, ships often worked in tandem with other ships to provide auxiliary functions and support capabilities. As a result, navies in general tend to be extremely bureaucratic and centralized, and log books are largely ubiquitous. If your ship is costing money through the ass, Admiralty is going to be pretty fucking upset if you embark on a voyage with no set purpose and out of the overall strategy.

In terms of tactical initiative, it varies over geographic and temporal terms, because the level of armament and shipbuilding technology, local weather, tidal, and supply conditions. However, it can be safe to say that in a tactical situation, skippers are permitted some degree of flexibility.

In terms of crew, you have citizen sailors like the Venetians or Athenians but chances are most of your crew are going to be uneducated scum and country rubes, because of the manual nature of their profession. Thus the senior officer will usually be the most educated man on the ship and his decisions are generally not informed by consensus.