Will payroll deposits show my salary while in Thailand affect my DTV application?

Do you mean you've been working in Thailand without the appropriate visa to allow you to do so legally? Fortunately for you this is unlikely to interfere with a DTV application at a Thai consulate. Just remember you will need a letter from your employer confirming you are allowed to work remotely and that you will have no interaction with Thai entities or anyone located inside Thailand

I don’t see why if it’s only a month or two. Thailand has annual leave, so getting paid while on holiday is not a foreign concept.

It obviously depends on the type of work you do and whether it could be interpreted as work performed in Thailand. In most cases this is not an issue in itself, but it depends on how it is presented and what you are applying for. For a DTV, the key point is that you can document stable income from abroad and that the income is not derived from a Thai employer or Thai source. Payroll deposits showing a foreign employer and foreign source are normally fine, even if some payments were received while you were physically in Thailand. You will in any case need to leave Thailand to apply for a DTV, and you should expect to be asked to document both a three months 500,000 baht balance and income from a foreign source.

So you did work in Thailand with a work permit and now think that your salary paid into your Thai bank account could be a problem?