Another user of kanjiVG here, and very much a non-expert on svg standards and recommendations. I did find quite a bit of evidence though that omitting the DTDs in the files and binding the namespace (using xmlns:kvg="
http://kanjivg.tagaini.net") is at least recommended practice (independent of the svg version it seems), see e.g.
https://developer.mozilla.org/en-US/docs/Web/SVG/Tutorial/Getting_Started (which however seems to assume svg v1.1 and says the binding of the namespace is mandatory).
So I would say there are two options here:
1. Only doing minimal changes: definitely binding the namespace, probably also omitting the DTD (if people here are fine with it)
2. Going to SVG 1.1 and also changing the ":" in the id attributes to "-" as suggested by verdy-p
It seems 1 already fixes a lot of problems, such as the broken images on Wikimedia, and should only really effect users who explicitly make use of the in-file DTDs.
Personally, I would also be fine with Option 2. The changes to my code, if any, would be minimal. But I can well imagine that this is more problematic and would be all in favor then for the solution proposed by Pascal Baillehache (have a tag/release for the last version in the old format).
Best, Dominic