According to the PM book" Debunking 9/11 Myths: Why Conspiracy Theories Can't Stand Up to the Facts":
“When contacted by Popular Mechanics, spokesmen for NORAD and the FAA clarified their remarks by noting that scrambles were routine, but intercepts were not---especially over the continental United States.”
This suggests a good number of scrambles did not lead to intercepts but PM never cited any numbers. There was this from the WashPo :
"..another federal official said that two years ago [in 2002], military jets could identify and intercept only about 40 percent of intruders in training drills. "
But that’s an anonymous source talking about training drills in 2002. According to a 1998 article on the Washington National Guard site:
“To hone its air sovereignty skills, the sector participated in numerous deployments and exercises during the judging period, including the Felix SPADE – Simulated Penetration Air Defense Exercises — program. During SPADE, the sector practiced 46 live no-notice airspace penetrations. The exercise tested WADS’ ability to detect, intercept, and identify a simulated unknown aircraft trying to violate national sovereignty. The sector was 100 % successful.”
100% Yeah right! No offense to anyone associated with the Washington National Guard but I doubt any such exercise could never fail, not even once unless the drills were somehow dumbed down.
According to an article the same year in American Defender:
“At the Southeast Air Defense Sector in 1997, weapons controllers tracked 427 unknown aircraft and intercepted "unknowns" 36 times. In the same year, the sectors in the Northeast and West handled 65 and 104 tracks, respectively.”
Unfortunately the word ‘scramble’ does not appear anywhere in the article but note that in 1997 (just 4 years before 9/11) only 8.4% of “unknowns” were intercepted in that sector; since it accounted for 71.6% of that year’s “tracks” the national percentage couldn’t have been that different, that alone pretty much torpedoes the truther fantasy that ‘other than on that day’ NORAD intercepted any aircraft going off its flight plan in 10 minutes. At that point the US had “10 fighter wings dedicated to our mission — 20 pilots sitting alert around the clock waiting for the order to fly when needed” that was 3 more units and 6 more planes than on 9/11 so we should expect performance to have dropped 1997 – 2001 especially in the northeastern US among the units deactivated was Burlington, Vt.; and Atlantic City, N.J. Shortly after 9/11 The Calgary Herald reported that “Last year, there were 425 unknowns -- pilots who didn't file or diverted from flight plans or used the wrong frequency. Jets were scrambled 129 times,” yet another torpedo! Only 30.4% of such flights led to scrambles! This also suggests that less than a 1/3 of scrambles led to intercepts which is close to the 40% cited by the WP for 2002 drills and fits with PM’s claims.
Parhaps someone smarter and/or more knowledgeable than me can massage this into a fuller answer according to a December 1999 article in Airman magazine (a USAF publication) “according to [“full-time alert pilot” Capt. Tom “Pickle”]Herring, Detachment 1 gets scrambled more than any unit in the Guard, averaging 150 battle stations a year and about 75 launches annually.” This once again reinforces the notion that not all suspicious flights led to scrambles427 tracks vs. 75 scrambles. IF “Detachment 1” had been the only one in SEADS it would be easy but the same article reported that “Besides Homestead, alert birds also sit armed and ready at Tyndall; Langley AFB, Va.; Otis Air National Guard Base, Mass.; Portland International Airport, Ore.; March ARB, Calif.; and Ellington Field, Texas,” and Tyndall presumably was part of the same ADS.