The unintended costs of a government shutdown

Just anticipating a shutdown wastes a great deal of time -- agencies must understand OMB and Justice guidelines, and then develop contingency plans for reduced activities. Those plans must identify which employees are "excepted" from furloughs and which are not; those who aspire to "essential" status but do not get it receive an unwelcome message. And when regular appropriations are delayed, uncertainty about final appropriations leads many managers to hoard funds; in some cases, hiring and purchasing stops.[...]

Over the long run, the shutdown could cause other costs. Now that contractors have learned they face a risk of interrupted work, they might charge the government a premium for this risk. Knowledge that furloughs are possible may also threaten the governments' ability to attract and retain quality personnel.

That's from Roy Meyers's "Late Appropriations and Government Shutdowns: Frequency, Causes, Consequences, and Remedies" (pdf).