I only mention those particular cities from a quick look at a map. I don't have specific conflicts or blockades in mind, other than recalling that Portugal, Spain and Venice had powerful navies, and that Batavia (Jakarta) was a major location for the East Indies trade.
Not sure if you mean naval battle as engagement of vessels at sea or what is the advantage of a harbour for a navy.
Assuming you mean the second then you have the obvious advantage of safe docking and protection against elements. If you mean tactical, up to almost the coming of steam and rifled naval artillery harbours provided a notable advantage for the defenders. If you try to enter it with an assault flotilla then you are going to end up under the cross fire of coastal artillery, normally placed in high ground. So they can engage you at a longer distance from a static stable platform,(either battery emplacements or forts) while you are swinging at the mercy of waves making yourself a poor fire platform, notably in the time of ships of the line.
If you manage to get passed them then you are under crossfire from the different angles from other batteries and those of the ships in the harbour throwing broadsides at you. Remember that to enter the harbour you have to use a specif sailing channel so you do not have much margin to manouver which makes you even more vulnerable to either avoid fire or return it yourself.