Calculating reserves, and the 50% rule
According to the rulebook pages on Deep Strike (p.36), I think the relevant rule-- for the sake of calculating 50%--is:


  When working out how many units can be placed in reserve, units that
  must be deployed by Deep Strike (along with any models embarked upon
  them) are ignored.


To apply to your situation, take your entire army and subtract (put aside mentally or physically) all the units that must be Deep Striking.  Whatever remains is the value that helps you determine 50%, so in this case corresponds to Case #2, 3 units (50 percent of 6 units) is your maximum reserve capacity.

EDIT: According to the General Rulebook FAQ v1.5, this is clarified further:

Q: Do units that are transported in a vehicle that MUST start in
reserve count towards the number of units that can be placed in
Reserves? For example, must I count the units in a Drop Pod or
Valkyrie towards the 50% of units I can place in Reserves?
(p124)
A: No.