Each encounter with a roamer is counted as a separate encounter, even if you’ve encountered them before or have done damage to it. Therefore, yes, a Quick Ball will have the heightened catch rate each encounter.
Additionally, everything about a roaming legendary’s stats is set in stone the moment they start roaming, before you’ve even encountered it in battle once. For Cresselia, her stats are set when you first interact with it in the overworld on Half Moon Island. The easiest way to hunt Cresselia is to save in front of its overworld sprite, interact with it, chase it down, then reset and repeat until it’s shiny.
If you’ve already done this, then it’s still possible to shiny hunt it, but there’s an extra step. First off, the Cresselia that you have currently roaming will never be shiny, and you have to reset it by KOing it and then beating the E4. After that, Cresselia will act as if you never triggered it at all, so just go to Half Moon Island and save in front of it, then start hunting like explained in the above paragraph.
Once you’ve encountered a shiny, it will always be shiny every time you encounter it. You can save and turn off your game and it’ll still be shiny when you come back.