Would 3 years of master's in Computer Science look bad in PhD applications?
I think in the current circumstances, taking a few months extra to finish your Master's will not be looked on negatively. It will be easy to explain in your applications (exactly as you have done here) the reason for the extra time taken. Overall, a thesis-based Master's will probably be better for PhD applications than a coursework-based one, as you will have more demonstrable research experience.