I sometimes encounter shrimp boats net-fishing off the bottom of Lake Pontchartrain. Never see day shapes, but I do know they can't maneuver very much at all and I behave accordingly. The tell-tale signs are a huge prop wash coming off the stern of a boat that's barely moving, and a really tight strain on the net lines coming off the side blocks.
But not all fishing boats are as obvious as this, nor do all other recreational boats "get it" in my experience. the commercial skippers are usually on the radio and get called by the f/v (sometimes to usually) and they work it out. Most rec. boats don't have, or don't monitor, channel 16 so they don't hear from the f/v til they're *really* close
Tugs and tows, especially on a wire, typically do show day shapes.
In practice, most courteous mariners use the "if it's easier for me to avoid him than vice versa, then I'll do it" method if the Rules of the Road don't give an obvious stand-on/give-way answer. but this is best concluded only after actual comms between vessels to sort it out. Guessing without comms can be dicey because you don't know how the other guy is guessing it.
Some of these situations do devolve down to Rule 2 (the "special circumstances rule"), if the situation isn't crystal-clear enough for the steering and sailing rules. Typical would be a multi-vessel situation developing, where each is arguably burdened as to one and privileged to another, or where evasive action might put you into worse trouble. You have to just "work it out".
Problem is, all this depends on everyone knowing the rules and how they work. Most don't, especially in the weekend boating crowd.
This has been an interesting discussion, and it was good to finally hear from a commercial fisherman. I hope we haven't beat this to death but it does seem there's a lot of misunderstanding on the topic.
My answer to Jack's question about "fishing" was a bit vague. I would guess the regulation's reference to "fishing" would apply to commercial fishing activities that restrict the boat's ability to maneuver? May depend on where it takes place. IIRC, the only commercial fishing activity that takes place in San Francisco Bay is a herring fishery, by gill nets, for a short period of time. If one is in confined water ways with commercial fishing activity present, that could compound the problem.
San Francisco has a large fleet of recreational charter boats operating in and outside the Bay. As they have many lines in the water either drifting or trolling they are somewhat limited in their maneuvering capabilities. When both sports and commercial fishing, I always tried to stay out of their way as much as possible. I guess they could be classified as a "commercial" fisheries?
The individual sports fishing boats have no special "right of way privileges", as far as I know. Bottom line, in my opinion, whether fishing or racing sailboats, is to give others ample room, safety permitting.