It was not just that Crystal. For a while he also used to have a handhigh ceramic figurine that featured in one episode and somehow survived said epi for about half a season. Can't recall what it was called. It nestled in a big one, together with others.
If you keep an eye on Picard throughout the series, you'll see that he very often had things in his hands while sitting at his desk. Mostly tablet computers and tea cups, granted, but also flutes, artwork, ancient weaponry, books, archeological findings and iirc even a small spaceship model.
Toying with items on our desks is such a normal behaviour that most of the time we don't consciousely notice it in others. I daresay, though, that we register it subconsciouely and that it adds to giving the character a more realistic dimension, more depth and personality.