If you sign a contract to commit war crimes, that's on you. However, it's probably a standard in merc contracts, that the mercs will follow the Ares conventions. If your employer demands that you break them, it's a contract breach; committing war crimes hurts your reputation, but the Z-league mercs trying to scrape a couple of C-Bills to rub together, are often blinded by the money (but at the very least ask for a significant bonus).
Not necessarily.
First, remember that all the Great Houses suspended the Ares Conventions at the beginning of the 1st Succession War. Even when they were in force, the Great Houses only paid lip service to some of them. For example, there were numerous infractions against Article I - Nuclear Weapons and Article VI - Biological Weapons. The Capellan Confederation were the first to ignore the rules during their war against the Taurian Concordat, justifying the breach by the fact that the Taurians were non-signatories. The greatest weakness of the Ares Conventions was the fact that it did not have any penalties for ignoring its provisions (nor was there anybody to enforce them even if they did). Not to mention that they were created to govern the conduct of nations not mercenary units. Why would they care to include the Ares Conventions in their contracts?
Second, during the SWs, to further their long-term plans ComStar subtly encouraged greater destruction by House and mercenary units alike and therefore had little reason to include the Ares Conventions. If they were included it was likely at the insistence of the employer or the hired unit not ComStar.
Third, there are several states that never signed onto the Ares Conventions, such as the Taurian Concordat so there was little reason for them to include them in a contract.
Fourth, given the failure rate of mercenaries units, desperate mercenaries will frequently sign anything just for a paycheck. The Great Houses were more than happy to use such units to complete work that they didn't want their own units to dirty their hands on.
Fifth, a mercenary unit that frees up employer troops to conduct atrocities may not be breaching the literal provisions of the Ares Conventions, just the spirit. However, just an association with the acts can extend the taint beyond the unit that committed the acts. Just look at all the Blakist employed mercenary units that suddenly became wanted fugitives after the Jihad broke out. Most did not get directly involved in the atrocities that took place but were still wanted by most of the Inner Sphere.