They could have a province type for land masses that are embedded to but not connected to nearby land which makes it difficult to take without naval blockade and difficult to maintain a naval blockade as well, this could cover lagoons, capes, atolls and some small islands close to coast. This could be applied to not just Venice but also some other provinces that historically served as naval fortresses, like those of Portuguese in East Africa, India and Southeast Asia, Dutch in Southeast Asia and China and British in various places. They could make these viable footholds for naval powers in general.
However it must be reiterated and emphasized that Venice is an extremely important state in this time period, especially now that start date has been pulled earlier to 14th century. It's not some minor power that can be treated as an unimportant afterthought or even with less attention than Gotland. It was the driving factor in many innovations, institutions, incidents and events in this period including several pivotal wars. Venice had the state revenue, military power and especially naval power to contend with bigger powers around it especially in 15th and 16th centuries. Venice keeps getting neglected despite its formidable power and impact in the first couple centuries (up to 1580s really) because it became mostly irrelevant in the second half of the game's timespan.
Ironically, in EU4 the second half where Venice is less important is also the period that most players don't play yet this hasn't stopped developers basically ignoring one of the premier powers in Europe in the most played half of the game. It's yet to be seen if this will be different with Project Caesar and whether the 1600s+ will be as popular when now the game starts significantly earlier.