The keywords for our site comprises of words which are google stop words
Is it better to write this as:
or does it make any difference?
Google is smart enough to know that "thank-you" and "thankyou" both mean "thank you". So trying to obfuscate it would be pointless.
Stop words are basically so common that trying to rank pages for them are pretty pointless. I wouldn't be optimistic about attaining rankings for them directly. Instead I would focus on alternative keywords that are synonyms and long tail search terms that use those search terms.
How do you know that the words are stop words?
Stop words have a very specific definition - here's Wikipedia's:
Stop words is the name given to words which are filtered out prior to, or after, processing of natural language data (text).
I can run a Google search for thank you and get relevant results and when I run a keyword tool analysis I see that the term "thank you" has about 4,090,000 monthly searches - that wouldn't work if Google were filtering these words.