"It's not going to be as much a driver of policy expectations as it might have been otherwise, so we wouldn't think it would have such a major impact on the Treasury market," said Ian Lyngen, senior Treasury strategist at CRT Capital. Lyngen said, however, if the number is a big surprise, the market will trade it. "But unlike prior employment reports, it doesn't feel like there's a great deal of positions put on ahead of it, and not a lot of risk being taken on either side."
(Read more: Why the Fed may not taper until 2014)
The economic impact of the shutdown has yet to be seen, but it has made the view of the economy murkier because of the lack of all types of government data, now scheduled to be released gradually. The shutdown was resolved last week when Congress voted to push deadlines for a spending resolution to January and the debt ceiling to February.
"We think this will be a strong report. We're looking for 200,000 payrolls and a 0.1 drop in the unemployment rate," said Dean Maki,chief U.S. economist at Barclays. "Pretty much everything we look at suggested stronger payroll growth in September, than in the prior few months."
Maki said the September report should be the first in a string of better reports, reflecting a better environment for hiring. "We have not changed our call for a December tapering. If we're correct then jobs growth is strengthening notably over the next three months," Maki said.
Because of the government shutdown and uncertainty, the market has shifted its view for when the Fed might begin to "taper" or pare back its $85 billion in monthly bond buying. While December is still an option, some Fed watchers do not expect the Fed to slow its purchases until Fed chair nominee Janet Yellen's first meeting in March, or even later.
Some economists see a half percent hit on fourth quarter GDP growth from the shutdown, which should be somewhat made up in the first quarter of 2014.
(Read more: DC gets busy on to do list to avoid another crisis)
On Monday, one dovish Fed official weighed in on the lack of data and the question of tapering the Fed's purchases of Treasurys and mortgage-backed securities. Chicago Fed President Charles Evans told CNBC's Steve Liesman that it will be "tough" for the Fed to have sufficient confidence in the economic recovery by December.
(Read more: Fed's Evans: Shutdown may delay taper)
When asked about the Fed tapering, he said the data pose problems. "October is a tough one. December? I think we need a couple of good labor reports and evidence of increasing growth, GDP growth. It's probably going to take a few months to sort that one out," Evans said on "Squawk Box."