The house makes money from rake. This means it's not in the house's interest to enable any cheating, since cheating makes the house less trustworthy, and therefore, there is less rake being generated.
Unfortunately the criminal mind discounts the possibility of getting caught. There have been several big scandals of this sort in online poker. Scams at Absolute, Full Tilt and others have been uncovered.
Most poker-room scandals are separate from the house cheating and more to do with bad accounting/book keeping practices and out right stealing.
The Ultimate Bet / Absolute scandal involved super-user accounts being used to reveal hole-cards of opponents and that most certainly was cheating.
The end result is that room went down in infamy and most of the people associated with it at the highest levels are looked down upon in the poker community.
On the other hand, Poker Stars ended up picking up the tab for Full Tilt, which is now a fairly trustworthy room thanks to Poker Stars' management.
Not to mention that fult tilt probably could have gotten away with it indefinitely if they weren't shut down. They were basically practicing a form of fractional reserve.