This is an interesting topic.
To your questions:
1) Is it safe? Probably not.
2) Can I be questioned by the software vendor? Probably not.
3) Can my paper be retracted from journals? Probably not.
You would have to be sure that you don't get caught. If you are doing your doctoral research at a bigger university you might slip through the cracks because somewhere in your univeristy is using a legit license of the software. In this case it is unlikely that the software company would actually investigate if you are using a license. If you are doing your doctoral research at a smaller university your work might be unnoticed and the software company won't investigate further. But Google Scholar will find everything in case they would want to investigate.
The software company could ask you if you have a license which would be their last step in the investigation. In most cases that happens when someone is using a company outside normal business hours or in a completely different IP range than normal. In your case the software company would only see you using a cracked license. I never heard about software companies who are creating simulation software actually asking reserachers regarding their licenses. But they are fully aware of some researchers using unlicensed software.
If your paper can be retracted from journals could depend on the journal guidelines. The software company would probably see it as some form of advertisement. I would be more worried about your doctoral thesis and your relationship with the university if $h!t hits the fan.
Side note: I know cases where researchers got licenses for simulation software from the software companies. If it's a good project they might support you and are interested to get the results published. They always want to see practical applications for their sotware published because that is the kind of advertisement.
Side note 2: What is wrong with your university? You are doing doctoral research with unlicensed software. Isn't your thesis advisor concerned with how you are obtaining results and the software you are using? And why did you get a research topic when your university doesn't have the actual tools for it?