Yes, Typically ammo BPV is factored in with the weapon system. However, with some WS having multiple rounds per shot (ie rocket pods) the BPV is found on the missile table. and you count the total number of missiles loaded.
Example
M159 Rocket POD (19x MK40 FFAR)
M159 Rocket POD = 0pts
MK40 FFAR = 2pts
Total = 38pts
So in the case of the M40 RCL you count the weapon system and each type of missile. Not the number of missiles carried. (counting ammo is exhausting! my 0.02ยข)
Example
M40 RCL
M40 RCL BPV = 1pts
M334A1 missile BPV = 13pts
Total = 14pts
or
M40 RCL BPV = 1pts
M334A1 HEAT missile BPV = 13pts
M494 APERS missile BPV = 15pts
Total = 29pts
Hope this helps