No, the order doesn't matter, both the slow and boost will be applied. However, the slow will always be more effective, so it's not necessarily worth to pop ghost while exhausted.
From http://leagueoflegends.wikia.com/wiki/Movement_speed, movement speed is calculated by:
Movement Speed = (Base Movement Speed + Flat Movement Bonuses) × (1 + Percentage Movement Bonuses) × Slow Ratio
E.g. if you have 310 base speed, your effective speed with both ghost (27% boost) and exhaust (40% slow) will be:
310 * 1.27 * 0.46 = 157236.4812
So no, the order they are applied does not matter;doesn't matter, the end result is always the same. However, the slow willis always be more effective, because it's a ratio of the effective speed with boosts.
From the example above, if exhaust wasn't applied, you'd gainnormally ghosting would give you 83.7
extra speed, however, when itif you ghost iswhile exhausted applied, you gain only 3350.482
speed.
Likewise, without ghost, the exhaust would subtractbeing exhausted normally subtracts 124
speed, but being exhausted withwhile ghosting ghost, it subtractswould subtract 152157.5
.
Another example; if you slow and boost yourself by an equal amount, say 20%, the net effect would be that you're slowed:
310 * 1.2 * 0.8 = 297.6