(chore): clean up use of spmatrix and sparray

[ilan-gold]

Please describe your wishes and possible alternatives to achieve the desired result.

At the moment, we use a lot of spmatrix and sparray as types where they shouldn't be used. We should clean up the types and do the promised deprecation on instance checking: https://github.com/scverse/anndata/pull/1616/files#diff-3b4874efa9bc9a522fa0cc5a88c69e233d7b46f2993331162bab12c4a6371bdcR70-R74

We should also look for other faulty instance checks