Do modern airliners have a flaps warning indication?
It could have been as you witnessed.

In 2005, a modification package dubbed Quiet Wing was offered for the 737-200 and the 737 Classic (-3/4/500) that would droop the flaps by 4° for all phases of flight.


  [It] decreases drag for cruise, and increases the aerodynamic efficiency of the wing by between 2% and 3%.


The NTSB in 1981 also found that many 727 pilots were doing the same thing in cruise—but manually and unapproved. They would pull a CB to keep the slats on the leading edge of the wing retracted, while the flaps extended to the their first stop.


  Investigators believed that 727 pilots (in general, and this flight specifically) were setting the trailing edge flaps to two degrees during high altitude cruise, while at the same time pulling the circuit breaker for the slats so that they would not activate. This configuration was rumored to result in increased lift with no increase in drag, thus allowing more speed, higher elevation, or decreased fuel consumption. Flaps and Slats were intended to only be deployed at low speeds during take-off or landing.


To answer the title question, yes. Flap position indicators exist, and combined with the electronic speed tape, the maximum speed indicated will be slower.

If the flaps were to be extended at above design speed, an overspeed warning will be triggered as well.