Unfortunately, earmarks aren't transparent at all in today's political world. Politicians continue to throw earmarks into random legislation bills, and these earmarks go unnoticed quite often. Even with watchdog groups scanning bills for earmarks, these political favors aren't transparent enough. If nobody notices a given earmark, then it slips through and wastes government money.
When allocating resources within the network transparency can be undermind while considering the interests of the multiple parties involved. What this means is that the directionality and purpose of what the tax money can be used is skewed and on top of that is not being transparently shared with the public, which is where in the firs place those resources came from.