Everything about it is a problem. Please seek legal counsel. 1st he needs a passport unless you're going to pay him cash under the table against the law. This would put you, your company, and partners at risk.
Secondly what kind of job is this because the work permit system is in place to encourage companies to hire thai nationals. If it's a job a thai can easily do there is a high chance it won't even get approved.
If you're saying you had 60 day VISAs both times and you are entering again for the 3rd time this year by Air then no there will be no problem. If you follow the rules and don't over stay your VISA you are good. I've been to Thailand 5 times in 2 years with no issues.