Is a civil union certificate accepted as proof of relationship for a spouse DTV visa in Thailand?

This is one of the things that's going to be HIGHLY dependent upon the embassy.

Here is an example: Currently Thailand does not recognize same sex marriage. But there are Thai embassies in countries that do recognize same sex marriage. Some of these embassies will actually issue a non-O visa based on being married to a Thai of the same sex, because it's recognized there. But as soon as that couple gets to Thailand, they cannot apply for an extension based on that visa because Thailand does not recognize the marriage.

Because with the DTV you shouldn't really ever need to engage with immigration, it's very possible that an embassy might accept this. But it's going to be up to the embassy, because they can decide to accept it based on the local customs, or they can decide to reject it based on strict interpretation of Thai law (which does not have civil unions).

The only way to know is going to be to check with your Thai embassy.

Short answer : No!