In theory, yes, Universal Binaries are bigger than their PPC-only counterparts. This shouldn't make too much of a difference as its only the executable part of the program that will get bigger. All the resources, localisations, and config files are still the same. Even for a very big and complicated app like PhotoShop the difference is likely to be less than 5mb.
Ten years ago this would have been a really important issue. Now, with the average user having at least 1000 times that amount of space free, its not really a problem.
By the way, the amount of memory used by the program is unchanged - the operating system loads only the code for the correct processor.