So there's cavitation which is fluid/gas moving quickly within the joint that makes noise. This is what's heard when you get a manual adjustment at the chiro. There's also the possibility of a "snapping" tendon/ligament or cartilage. In the shoulder, this could be from the biceps tendon popping out of the groove, but not the only reason. The former is okay if it doesn't happen all the time, the latter is not. The reason I say it's okay if it doesn't happen all the time is that cavitation can cause damage where the gas bubbles pop, but this is implied from mechanical instances where cavitation is seen. Now, in the case of snapping tendons or cartilage, some people can have flapping cartilage that doesn't cause them any pain, but with the right combination of movement direction and compression pressure, that cartilage can rip, getting lodged in the joint and then there's real problems! Snapping tendons and ligaments will get thickened and lose elasticity making them more susceptible to frays and tears.
The point is still the same, if it doesn't hurt, you're probably okay. I wouldn't try to make the noise on purpose, as that just seems like you're asking for trouble, but unless you're willing to have an exploratory scope or an MRI done, I don't see the point in worrying about it.