I guess I'm the main contributor to my own thread here! My research is turning up interesting tidbits of information that I'll share with you as I find them. As always, your comments and additions are very welcome.
The first fact comes from
The History of The Hobbit; in Tolkien's early version of that passage, the Dwarves' instruments were originally somewhat magical in nature. The fiddles and flutes were brought out normally, but
Quote:
...Bombur produced a drum from nowhere; Bifur and Bofur went into the hall and came back with [their] walking-sticks and turned them into clarinets...
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Rateliff also mentions that later in life, when thinking about revising
The Hobbit to harmonize with LotR, JRRT noted to himself,
Quote:
What happened to the musical instruments used by the Dwarves at Bag-end?
Why did they bring them to B-End?
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and goes on to say, "Even thirty years later, he was unable to come up with a satisfactory answer."
Actually, I have come up with the answer to the "what happened" - when the ponies were taken by the goblins, it is said:
Quote:
And that was the last time that they used the ponies, packages, baggages, tools and paraphernalia that they had brought with them.
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If nothing else, the instruments would surely be classified under "paraphernalia". Since I have not been able to find any references to the use of musical instruments by goblins/orcs (aside from percussive whip effects - see the animated movie's "Where There's a Whip, There's a Way"!

- and similar use of weapons) I assume that the instruments were destroyed, perhaps taken apart for any materials of value that they might have contained.
More to come in the next days - I'm now working my way through pertinent references in Sil, UT, and HoME as well as LotR.