I'm not sure of the exact implications, but what I do know is that SCI is required to work in certain agencies or areas that handle restricted technologies and methods, such as the NSA with SIGINT:

"For access to information at a particular classification level, individuals must have been granted access by the sponsoring government organization at that or a higher classification level, and have a need-to-know the information. The government also supports access to sensitive compartmented information (SCI) and special access programs (SAPs) in which access is determined by need-to-know. These accesses require increased investigative requirements before access is granted" (Wikipedia)

So if you don't get SCI, any career within Federal intel community would be stunted.