It's important to recognize that there are at least Five (5) parties involved in an acquihire. You have the Acquiring Company, You have the Investors in the Acquired Company, You have the Founders of the acquired Company, You have the employees of the acquired company and, you have the employees of the acquiring company.
All of these parties come into the mix in an acquihire.
The investors have preferred shares, quite often with a liquidation preference, and they will always get something. The founders will often get something, (though in the case of liquidation preferences, it may not be very much - "consulting bonus" is not uncommon here) in an acquhire. The employees of an acquihired may or may not get totally screwed on their common shares depending on the size of the liquidation preference of the investors. They will almost always get a "retention bonus" - that may be on the order of a 50% of their salary, repayable if they don't stick around for 1-2 years.
All companies I've worked with have been pretty good about leveling salaries, and are careful to avoid a situation in which you have two groups of people doing the same job, but one group making 50% more than another. You may have isolated situations in which an employee or two is out of wack on their compensation, but companies like Yahoo! try hard to avoid having systemic disfunction in compensation. The mechanisms for getting new employees in a tight job market come in the form of hiring bonuses and/or acquihires.
Reading your comment carefully, I think you are considering the scenario of an acquhired where most of the employees acquired were founders, whereas I'm thinking of the 30-50 employee company, where only a couple of the employees were founders.