The impact of a brief shutdown – or even just the threat of one – for government contractors can also mean higher costs for federal agencies in the future, although it's almost impossible to assign a dollar amount, says Roy Meyers, a political science professor at the University of Maryland Baltimore County and a former CBO analyst.
"It can reduce the profits of the contractors," says Meyers. "And the next time they consider working with the federal government, they count that as a risk, and they charge more."
That impact could be felt acutely in the Washington, D.C., area, where many contractors are based. And that could be compounded by the impact on tourism in the District as federally-funded museums and monuments are shuttered. The shutdowns of the 1990s cost the District of Columbia an estimated $50 million in lost business and cancellations, officials said at the time.
There's also the issue of back-pay for furloughed workers. While only those workers deemed "non-essential" would stay home during a shutdown – about 40 percent of the federal workforce during the mid-1990s – there's a precedent for lawmakers granting those individuals their pay once the government is back up and running, even though they weren't producing any work.
Cost estimates must also factor in delays in the collection of fines and fees typically gathered by federal agencies.
OMB said after the twin shutdowns in 1995 and 1996 that $2.2 billion worth of licenses for U.S. exports were delayed and that some $60 million in environmental fines and settlements were not collected or negotiated.
(Read more: Why markets should pray for a government shutdown)
Most of those fees eventually get collected, says Yandle, but the delays and the inconvenience to businesses and consumers can end up having resonance that won't show up in cost estimates at all.
"Those costs that cannot be estimated are often much more important than those that can," he said.
Meyers argues that a shutdown's cost to the budget or the effects on the overall economy estimates – flawed as they may be – pale in comparison the societal cost of a government that seems bent on playing political chicken rather than focusing on solving problems.
"The real costs are really not in terms of consumer confidence or any of the standard measures in macroeconomics or even the federal budget," he said. "The real costs are in trust in government and belief that government officials are paying attention to the real issues of the country."
—By Carrie Dann of NBC News