They did get surreptitious DNA samples, because they did not want to alert the guy to their presence yet and have him flee before they could further investigate him.
The problem was that they needed buccal samples, straight from inside his mouth, not contaminated from a paper cup or something, to compare with the limited amount of DNA they had been able to derive from the mixed sample they had from JonBenet's underwear.
It was commingled with her own blood and had to be separated to ID it. Lacy said that was why they had to bring him to Boulder to get that non-contaminated saliva sample from inside his mouth.
The DNA coaxed apart from JonBenet's was said to be from male Caucasian saliva.
I'm not sure the DNA sample is even good enough to hold up in court. The fingernail DNA is said to be a weak sample and the panty DNA had to be separated from JBR's blood. A good DNA defense expert could probably shoot holes in them to cause reasonable doubt if the prosecution had nothing else to pin a suspect to the crime.
We may be seeing just how unwinnable a conviction really would be in this case - at least if one sticks to the intruder theory. As to the "family did it" theory, there's DNA all over the place but easily explained away. Apparently there was not even enough evidence for a grand jury to indict the Ramseys so that case is weak too.
I'm having doubts this will ever be solved.