Not to be dogmatic but you must be using ISO 639-2, not -1.
Looking at the list of
ISO 639-2 I found out that "Low German" also is dubbed "Low Saxon" there, and "Saxon; Low"
is actually in Calibre, one just has to start writing "Sax…".
Problem solved, thanks!
I'd only suggest, that you change the displayed name for "nds" to "German; Low" when you get around to it -- I suppose that "Low Saxon" is counterintuitive not just for me, but for most users, especially those from other provinces than Lower Saxony, where the language is used, too.
And it would be nice to have it pop up, when one starts with writing "German", as the other subsets do.
As for further differentiation, I'll take your advice and use tags!