What I'd suggest:
1. Let all ships carry troops.
2. Let merchant ships, you know, steer trade better.
3. Let light ships have the best blockade rating.
But most of all:
4. Create a system of naval interception at sea, so that there is a chance two enemy ships could, in fact, pass in the night. Sorties from a blockaded port would have a far higher chance to be intercepted. Chances to encounter an enemy in a deep sea area would be decreased.
Edit:
5. Also, allow "mercenary" ships you can hire. If you want to bolster your fleet with a bunch of merchant ships for a quick transport mission — do it! Make is so that the cost-to-purchase is lower, but the cost-for-maintenance is higher than a regular naval ship. (This came up when they first announced "privateering," which isn't really privateering the way it is implemented.)
Blocking ships within a port was a 'thing' though.
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