Yes.  In fact, lipid deposits are seen more often on silicone hydrogel
lenses than protein deposits, which is the opposite of what one sees
typically on standard hydrogels.

Large amounts of lipid deposition or protein deposition can be seen on
silicone hydrogel lenses.

As far as the "2 weeks", that is a generality -- some patients can do
well wearing them longer than that, some can't do well even after a
week.  I am moving more and more of my patients from a multipurpose
solution to a hydrogen peroxide based system (e.g., Ciba's ClearCare)
in order to keep their lenses comfortable for the full replacement
schedule timeframe.

How do you know how long you can wear them before you need to change
them?  Well, it's just like brushing your teeth -- just like you wait
until they hurt before you brush them, you wait until the contact
lenses become uncomfortable before you change them.

Seriously though, change them per your eye doctor's schedule not when
you feel like it or when they start to become uncomfortable.

Also, silicone hydrogel lenses tend to let you know when they are
dirty a little quicker than hydrogel lenses do.  I have quite a few
patients who complain that they can't wear their "2 week" silicone
hydrogel lenses for 3-4 weeks like they could their disposable
hydrogels.