This has been a problem mentioned on-and-off for years before Colonisation came in, of course.
Pretty much any story event happening in an uninhabited system got the same "what were those letters and numbers again?" problem. Numerous systems were made inhabited in the 2015 Horizons release and still have a "Col 285 Sector" name. I suspect that Frontier have never bothered to remove the limitation that system names require a client update, which would make any sort live renaming as part of colonisation quite a bit of extra work, and means that even story-significant systems (like the Marlinist colonies) only got renamed long after anyone really needed to visit them.
Personally, I'd be quite happy for Frontier just to give all inhabited-so-far systems currently with just their default AB-C d1-23 name a procedural-but-pronouncable name as a routine part of client releases. I don't have any interest in naming my system anything specific, but I'd quite like it to have a name of some sort. The question then is whether Frontier's existing procedural name generators can actually cope with another 100,000+ named systems (we're not there yet, we will be)