Permanetly - No (at least not to my knowledge).
Temporary - Yes. As tracks and roadbed are being replaced there are slow speed orders in place if the concrete for the roadbed hasn't been poured yet (or has been pured but hasn't set/cured yet). It also may apply to areas where stations are being refurbished and crews are using the tracks to work on the edges of platforms. The FastTrack program has been taking care of a lot of the "deferred/lack" pf maintenance issues that had existed.
As work continues on the tubes between Brooklyn and Manhattan as well as between Queens and Manhattan (due to Sandy damage), there are slow speed orders in sections that are being worked on (even on days when no work is being performed). The most current is the Cranberry St tube (A, C lines). On weekends the A and C are rerouted vis the Rutgers St tube (F line) between W4th and Jay St. During the weekdays the trains use the Cranberry St tube as normal but at slower speeds. Similar restrictions are in place on many weekends for the E train in the 53rd St Tube. The E is routed via the 63rd St tube (F line) and then via 6th Av to W4th where it returns to regular routing to WTC.