Do Air Passenger Number statistics on a route refer to both directions of flight?
By looking through the BTS website you linked (and is cited in the Wikipedia listing), you can find the answer.
The first 3 sections on the infographic; Summary Data, Carrier Shares, and Total Passengers include both departure and arrival passengers totaling about 14 million passengers.
The fourth section Top 10 Destination Airports (US Only) is less clear and you can't cross-check to the other totals because it is limited to only the top 10 airports. But it is a clue that the title says Destination Airports which implies departures only.
But there is a potential check. At the top, you can select the airport. By selecting Orlando, FL: Orlando International from the pulldown, you can see the data from there. That shows in the Top 10 Destination Airports that PHL is number 3 and the total number of passengers is 539,900. Since this is different than the 548,320 PHL-MCO number, it would appear that section references departures only.