Is it okay to include a very long appendix (for MS thesis)?
This does not sound unusual to me. Just ask yourself, is there a possibility that the reader would need this?

I have seen theses and dissertations with no appendices and some with over 50 pages of appendices. In my field, these are often filled with user study materials, source code, or raw data which can easily eat up many pages.

I don't see any harm done with being conservative and including everything. In this case, I have seen people list two versions of their thesis online, one with and one without the appendices.