In a standard pin tumbler lock, adding master wafers (pins) does make them easier to pick. They create more shear lines as you said & the more shear lines available, the easier the lock is to pick. For this reason, master key systems are usually designed to minimise the number of master wafers used.
Things are a bit different when it comes to an SFIC core, like a BEST. Whilst there are more pins present in each stack, if a lock is combinated such that there is only one operating key & one control key, then the presence of the extra pins in each stack does not make the lock easier to pick & in fact often makes it harder.
This is because there are two physically distinct shear lines. Unless one of these cylinders is master keyed, there is only one split in the pin stack that can be aligned at the operating shear line & another that can align with the control shear line.
When tensioning a BEST core (using a standard tension wrench), there is usually tension applied to both the operating & control shear lines[EDIT : this is not the case, see post by Xeo below]. This means when picking you can end up setting some pin stacks to the operating shear line & others to the control line & it is impossible to feel the difference between the two[edit: although it can be tricky, it is possible to ascertain which shear line you are dealing with]. Unless all pins are set to one shear line or the other, the plug will not turn. This is what can make a lock with multiple shear lines harder to pick than a standard pin tumbler lock.
There are special tension wrenches that are designed to only apply tension to the control shear line.
The term master wafer is used interchangeably with the term master pin.
The pin that touches the key is usually referred to as a "bottom pin", and master wafers for the operating shear line are placed directly on top of the bottom pin. Next is the "buildup pin", sometimes referred to as the "control pin" & finally there is a "top pin" on top of that. The length of each pin stack is supposed to remain constant, so different sized top pins are used, depending on the total length of the other pins.
These links contain some useful pictures & further explanation :http://www.keypicking.com/viewtopic.php?f=95&t=9460http://www.crypto.com/photos/misc/sfic/http://kstoerz.com/locksport/Schlage_SFIC_manual_Dec_2007.pdf
There is also a type of lock that uses multiple shear lines in the same manner as a BEST lock, but both shear lines are used to operate the lock, these are called master ring cylinders & they allow master keying without the decrease in security that is normally caused by using master wafers.
Hope that helps,