Did you install the second hard drive yourself? If so then your best bet is to swap your SuperDrive back in before taking it in for service.
I cover this scenario in more depth with this answer:
Apple's warranty (AppleCare) is specific about what components are
user replaceable/serviceable. The hard drive on an older MacBook for
instance is user replaceable, AppleCare used to have the option to
send you a replacement hard drive along with a disposable ESD
wriststrap for you to install it yourself.
The difference though is the hard drive in the MacBook was almost as
easy to access as the RAM in the Mac mini. The Mac mini's hard drive
is a different story. In order to access it you have to expose the
logic board which increases the chance of damage from ESD if proper
precautions aren't taken. Because of this the only user replaceable
part in the new minis is the RAM, since the logic board is still
pretty well protected when only removing the RAM.
The Magnusson Moss act essentially says they can't deny warranty
unless they can prove damage. It wouldn't be hard for Apple to say
"The upgrade situation you described to us implies that there was a high risk for ESD damage, which has likely caused such and such
The flip side though is that if an Apple Authorized Service Provider
(AASP) installs a third party hard drive your AppleCare will remain
intact because the AASP has proved to Apple that its technicians
follow all safety rules and procedures when working on Macs,
essentially the same reason Apple allows them to perform warranty
work. Apple would then not be involved in the hard drive's warranty
(though most HDDs have 3-5 year warranties of their own) but the
remaining components would still be recognized as "in warranty" by
Apple. The most you would need to do is provide a receipt for the
service you had done at an AASP.
source: I was "that guy" at the Genius Bar for several years who had
to turn people away from warranty coverage for unauthorized upgrades &
repairs. As soon as your Mac goes out of warranty I definitely
encourage a DIY attitude, however I would try to heed the above advice
while it's under AppleCare.
Basically if it was a user replaceable part (it's not) you wouldn't run much risk of them blaming a failure on your upgrade. The problem though is that with the optical drive not being considered a user replaceable component, and the replacement being a somewhat major (in their eyes) modification, they have every right to deny coverage since they have no way of knowing if proper ESD precautions and whatnot were followed.
If I were you I'd play it safe. The Superdrive installation isn't terribly difficult and could save you a lot of arguing if you don't get a Genius who just looks the other way.