It is not uncommon to see a frame based site of 100 pages or more be represented in some search engines by only its home page. Diana Botluk of LLRX.Com has also contributed an excellent article about the Invisible Web. Info pros have always done this with print tools. The challenge is to develop collections of Invisible Web sites just like we have always done with print resources. A huge issue is the lack of commonality between interfaces, syntax, and capabilities.
Every tool is different.
Consider each search tools as you would an individual reference resource. A great way to become familiar with and Invisible Web resources is to do preemptive searching. The lack of .pdf content indexed by the general tools. Especially important in a busy office situation. A great deal of U.S. Government data resides in Invisible Web databases.