This is where privateering comes in... these issues existed in the past and are hard to solve. Privateers gave the state the ability to look the other way.
You might make treaties with larger nations who could use various other negotiation methods (or, failing that, navies) to try and reach a global balance.
Why would a "larger nation" such as China agree to such a treaty when they can blow you out of their waters, and you can't blow them out of yours? What's in it for them? It's not in their interest, so a treaty is a non-starter.
A big nation doesn't give a shit about a small nation unless there's something in it for them. I.e. if they're a part of some pre-existing union, or if they host their military bases, or something else. And there's zero chance a big nation will risk going to war to protect a small nation's fishing rights, unless a war was already in the cards (in which case it might be used as a rather desperate "casus belli").
maybe just destroy their fishing equipment, there will be aftermath but I can't imagine the narrative "Ecuador's military going all over to the China sea to bully civilians" makes sense to anyone.
As someone pointed out above you can board them. I suppose an argument could be made for sinking them; it would prevent reclamation of the vessel for fishing later.