There's a bit more justification on at least string instruments. Strings have a definite change of timbre after enough time.
And the bridge might settle a little and the pegs need to settle in, etc. Any instrument that can be affected by humidity and temperature can be affected by time at humidity and temperature. I'm pretty sure there's not a lot of point in "burning in" a brass instrument but I've been wrong before.
Some brass instruments are valued because of better quality metals (more pure alloys - a bit of any oxymoron i know -, different valve systems, etc), but woodwinds almost exclusively devalue because they fall apart (wood vs. hot, sticky, bacteria infested air), and brass instruments tend to devalue on the whole as well. The good news for them is that new wind instruments are considerably less expensive than new string instruments. A custom made, top-of-the-line Trombone will cost you less than 10 grand unless you're REALLY trying to burn your money. Oboes and Bassoons are more expensive, but also tend to have more resale value as second-hand for students. to compare oranges to oranges, a new, top of the line Bass could cost you over 40k, or more. And basses are considerably cheaper than their smaller cousins. String instruments change a lot in the first 2 years. I can only really speak for basses, but having owned two new instruments, the Low end in particular takes time to develop. Slowly you start to notice the D string sounding great, then the A string. Eventually you start to get some real subterranian shit going on, and the viola section can feel you in their chairs. My current bass just hit it's first birthday a few days ago, and it's low 5th string is still working on being "played in". I've heard, for string instruments, that the process has to do with "disorganizing the longitudinal wood fibers", but fuck, idunno. Bass sounds good, I play it, i get better at playing the bass, one day I don't suck (hopefully).
yaaaay lack of resale value. at least I have the consolation that if I fail as a musician and a person I can sell my bass and get a year's worth of living out of it. Either that or I can burn it to keep myself warm.