A tourist visa is not designed for extended stays, so yes, going in and out of the country not only goes against the visa's purpose, but also, if you do it enough times, it'll probably raise some flags.
The tricky part that I see with your situation is that you want to live in one country, but work remotely for a company outside of that country. If your company has a base of operations in Thailand, you can get a business visa, which most countries will offer.
Some countries have self-employed visas which allow you to stay there with the only requirement being that you show proof that you can sustain yourself financially.
Some countries have entrepreneur visas that require proof of capital and an intent to establish a business in said country.
Some countries have visas for people who want to stay there for a long time, with no other requirement.
Since you're saying the company might hire Thai citizens, some countries also offer visas for people just evaluating a country for a potential place to start (or extend) a company.
I'm sure you've already done your research, but I suggest, if you haven't already, that you contact an immigration lawyer in that country to see what your options are; it's a worthwhile investment, and if it results in you getting the appropriate type of visa, then it saves you money from the plane rides and inconvenience of leaving the country every 30-60 days.
In these situations, especially if it can result in the company you're working for to get involved if things go south, it's best to err on the side of caution.