Well, it depends on what the non-standard instrument is. Cowbells are in fact offered in percussion catalogues and come in a selection of standard sizes, but most orchestras will still authorize individual players to purchase instruments on a case by case basis. The more popular a piece is, the more likely an orchestral will add unusual instruments to its arsenal. The cowbells in Mahler (and Strauss's Alpine Symphony) offer an excellent case in point. I would be very surprised if most major orchestras don't own a good set by now, and equally suprised if many of them were not individually acquired in some non-conventional way.
If the requirements are particularly strange, sometimes the instrument may be included with the music. The nightengale in Respighi's Pines of Rome offers one example (the music comes with the necessary recording), and you used to get the four taxi-horns from An American in Paris with the parts as well. Now you can also purchase them separately for a ridiculous fee. The last time I played the piece about a decade ago they wanted $400+ for the set, so I went down to a wonderful brass junk shop in SoHo (Manhattan) and got four wonderful antique car horns of nicely differentiated pitch for $30. Similarly, most orchestras will keep complete sets of antique cymbals (crotales) for such works as Ravel's Daphnis and Chloe, but many percussionist will own just the few pitches needed for, say, Berlioz' Romeo and Juliet or Debussy's Afternoon of a Faun. And contributors here will all be familiar with different realizations in concert of the Mahler Sixth hammer blows (I used a real sledge hammer on a hollowed out tree stump). The best hammer I have heard was Philadelphia's--sort of a giant woodblock set into an elastic cradle, not too large, but phenomenally deep, resonant, and characerful (I'm not counting Zinman's electronic solution).
Certainly there's no need for anyone to scrutinize the quality of the instrument--what matters is how it sounds. If the sound is right, then there's no issue. There are a lot of very expensive, nice looking, and "official" percussion instruments that sound terrible. I once had a very tough time trying to get a good set of bells for the finale of Berlioz' Symphonie fantastique. Tubular chimes aren't really dark and creepy enough--you want a touch of impurity to the tone--and bell plates don't have the overtones or sufficient carrying power. Real church bells are out of the question--they weigh literally tons, though the NY Phil has a set on wheels (they used one memorably at the climax of Also Sprach Zarathustra and nearly killed the last stand of second violins). So I went to a plumbing supply warehouse and started banging on pipe remnants until I found the tone and pitches I needed. Bell sounds are always a problem, and no two orchestras seem to have the same instruments.
In sum, all percussionists have to be prepared to improvise as necessary. It's part of the business.
Dave H