Intruder alerts might be largely based on detecting penetration rather than presence, and if the means of penetration is innovative enough, it will go unnoticed. Quite possibly, countermeasures or even detection mechanisms for transwarp beaming will not be invented until several decades into this new timeline...
I agree up to a point BUT in order for long distance transporting to work, sensors in NuTrek have to be far more effective than in previous incarnations (and they made no adjustments to the technology to accommodate the transport) so we have a discrepancy. I can't recall if the Enterprise detected the unauthorised transport or the hatch opening in engineering in the last movie. I think it was the latter, which implies that the Enterprise doesn't have automated systems to detect incoming transports.
I think the Narada, with its advanced tech, should have been able to detect the 'secret' transport but then there were lots of other ways that they might have been tipped off -weapons fire, unexpected access to computers etc.
Maybe Praxis blew up while the Klingons were trying to reverse engineer Narada tech. It's possible that they might have some nasty surprises for the Federation up their sleeves.
There are quite a few situations where 1+1 don't quite equal 2.