I haven't played a ton of courses that have permanent pins, but my current "home course" complex has two excellent courses that pull off the two permanent pin thing with excellence. (Seth Burton Memorial DGC and Orange Crush) Baskets are color coded and high quality, and not at all confusing. The way I see it, it's a luxury and shows the dedication of the community to the course. It ain't cheap to buy an extra 36 Discatchers for the course, so how can anyone really complain? Also, it means I can show up on any day and play any layout I want. I've played many courses with rotating pins, and they're great, but I always gravitate toward courses in their more difficult layouts. Those are the holes against which I want to test my game. It's a bit of a disappointment showing up at a course to challenge your game only to find that 450' killer par 3 is set up in a more open 325' location. I no longer have the option of competing against that more challenging hole. Again, in EVERY course I've played regularly that features rotating baskets, I have at least one hole that I prefer in a certain pin location.
The two permanent pins do offer a minor problem, of course. Particularly if one set of pins is longer than the other, it's very easy to find one basket blocking the path to another. Just recently, I had a "perfect" approach to a long basket deflected by the rim of the short basket, and during a tournament, no less. Bummer. I guess the short basket is now kind of like a tree/obstacle blocking the path to the long one, but it somehow feels different when your shot is ruined by a disc golf object rather than by a more conventional obstacle. I didn't hear the pros complaining about that feature of the tournament, but it's probably just because I wasn't hanging out with the pros...
I've played at least 5 courses blessed with permanent multiples, and I'd say it has NEVER detracted from the course. As others have mentioned, I find it far less confusing to navigate. On the other hand, I've played many more courses that have multiple rotating pins. On those courses, I very frequently think, "man I wish hole 18 was in the other location today." This is true both for one-time visits to new courses and for courses I've played week to week.
In summary, here are some obvious factors that make permanent multiples work:
1) Need the money to buy extras
2) Need good color coding or other aesthetic differentiation between tees
3) Benefit from course design where one basket is not in the "fairway" leading to another basket
And in case you're wondering, here are the five courses I've played with two permanent pins:
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Waller Mill Park in Williamsburg, VA - this one might just pull it off the best, both in terms of color (Mach/Chainstar and Prodigy baskets) and design (one basket rarely interfered with the path to the other)
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Orange Crush in Fairmont, WV - one of my favorites but one where the short basket becomes a fairway obstacle to the long basket in at least a few holes
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Seth Burton Memorial DGC in Fairmont, WV
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Bayville Park in Virginia Beach, VA
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Munden Point in Virginia Beach, VA