Is "佳能" the standard translation for "canon" in a religious sense? Apparently "巴利佳能" is the translation of "Pali Canon."

When referring to the foundational documents of other theological or philosophical schools, will I be understood if I use the term "佳能"?
No. 佳能 is only used for the translation for Canon the brand/company name.

There are more than one translation for canon in religious sense based on its different meanings. The standard translation for Pali Canon is 巴利文大藏经 (Wikipedia). 

If you are interested in the translations for other meanings, you can find them in a dictionary. Another way to find out is on the Wikipedia disambiguate page for 'canon', choose the term you're interested in, and click on 中文 on the left to see the Chinese version.