From the manual;
Flight Deck catapultsFlight deck catapults may be installed on
any carrier after the technology has been
researched. Note that this type of catapult
has different effects and rules than the
trainable catapults that are installed in
surface ships. Flight deck catapults can only
be installed on carriers. Flight deck catapults
will increase the spot value of the carrier.
Carriers with flight deck catapults do not
need to turn into the wind when launching
fighters on CAP or planes flying recon
missions. The number of flight deck
catapults that can be installed is limited to
two unless “Angled flight deck” has been
researched.
tl;dr - They let you launch CAP and recon without turning into the wind. They also increase spot value.