Potential consequences for a PhD student using a cracked software
Usual disclaimer: I am not a lawyer and this is not legal advice.

Several things to consider here:


It is the university's responsibility to maintain their computers, including their contents. So if your friends have been using a computer provided by the university with cracked software on them, the vendor of the software will go after the university first. They just want to get paid what they're owed, so it's better to go after a large university than some broke students. 
Normally, the university should have only provided students with user accounts, which do not allow the installation of software, which in turn is to be done by IT personnel with admin accounts. If they don't do this, shame on them, this is poor practice that warrants some fines here and there (and the cost saved with IT employees probably makes them insist on the poor practice).
If students had admin accounts to these machines, they have probably signed a contract/memo/agreement claiming they'd be responsible in such situation. Bad for them, but the vendor will prefer to go after the university first.
Part of grant money and department budgets are precisely meant to pay for tools required by research activities, which nowadays always include computers and software. There is no excuse for using cracked software over the long run.
To be clear, this is a matter of money, not of academic merit. As long as your friends behave during the process, they should expect to be fined, but not expelled. The university will come after them if they receive a fine from the vendor.
"Normal practice" (which I'm not endorsing here) when using pirated software for your academic work is to use it only in your personal machine and only if the department owns licenses for said software. In some large universities, they might even have "campus licenses" for software, making this ideia completely useless. The point is that you have the right to use the software, as your department paid for it, but instead of using it during office hours, you might prefer doing it from midnight to 6 am in the comfort of your bedroom.
If nobody has the license for the software, you might be in trouble to publish results obtained from it. But then again, you can first obtain results, then the license, then attempt a publication. You might even just ask for a trial license.
If these computers were owned by the university, there is no breach of privacy here. If they were owned by the students, IT should not have nosed around these machines without the students permission. And by the way, never grant someone the right to audit a machine of yours, specially if unsupervised. Everybody has secrets/nudes/browser history/work worth keeping private, all of which should only be kept/done in private computers.


My bet for the outcome (and please update your post in the future to inform us):


Students get away with a warning.
Advisor gets a warning and needs to spare budget to acquire the license, if the license is affordable. Otherwise, activities using this software will need to be dropped.
Story gets muffled, people will go around saying "It is yet to see what happens" until everyone forgets about the case. Then people will simply stop talking about it. This is to avoid having precedence of cracked software usage and preventing it from becoming common place.


EDIT
Just as an extreme example, there are software licenses that costs millions of dollars. Paying a fine over the value of license would warrant firing the professor who allowed its pirated use, as long as the university indeed pays the fine (unlikely) and had good policies to avoid it in the first place (further unlikely).

There is also software whose commercialization is restricted due to national security risks. Missile simulation tools come to mind. Here there is more than a "money problem", there is illegal usage of a controlled piece of software. But I'd hardly expect this to be the case.