For labels, the codes crh-latn and nds-nl are lowercase (see this query). For sitelinks, they are written crh-Latn and nds-NL (see this query).
Since language codes are case insensitive, they are both valid and equivalent, but I think we should be consistent, because that's what most users will expect (e.g. not one of the example queries use lcase() or ucase() when using lang() or schema:inLanguage - people just assume that a language code will always be capitalised the same way) and being inconsistent leads to unexpected behaviour (unexpected results when comparing labels with sitelinks is how I discovered that the capitalisation differs). I think only crh-latn and nds-nl are affected for sitelinks, so far less data would be affected by lowercasing those compared to changing the case used for labels/descriptions/aliases.
Review June 21, 2021: suggested update to Wikibase.default.php#199 (canonicalLanguageCodes) (currently, there is "crh-Latn"):
'crh' => 'crh-latn', 'nds-NL' => 'nds-nl',