From the Apple Limited Warranty:
EXCLUSIONS AND LIMITATIONS
This Limited Warranty applies only to hardware products manufactured by or for Apple that can be identified by the "Apple" trademark, trade name, or logo affixed to them. The Limited Warranty does not apply to any non-Apple hardware products or software, even if packaged or sold with Apple hardware. Manufacturers, suppliers, or publishers, other than Apple, may provide their own warranties to the end user purchaser, but Apple, in so far as permitted by law, provides their products "as is". Software distributed by Apple with or without the Apple brand name (including, but not limited to system software) is not covered under this Limited Warranty.
This warranty does not apply: (d) to damage caused by service (including upgrades and expansions) performed by anyone who is not a representative of Apple or an Apple Authorized Service Provider ("AASP"); (e) to a product or part that has been modified to alter functionality or capability without the written permission of Apple; ...
From the AppleCare Protection Plan:
b. Limitations The Plan does not cover:
(ii) Damage to the Covered Equipment caused by accident, abuse, neglect, misuse (including faulty installation, repair, or maintenance by anyone other than Apple or an Apple Authorized Service Provider), unauthorized modification,...
So it sounds like replacing a hard drive would not be covered by the warranty or the AppleCare, but since the hard drive is not an Apple-branded component, it sounds like it's not technically covered by the warranty anyway. Of course, they can choose to replace a defective drive, but it looks like the "fine print" gives them the option not to.
In any event, there's not a clear statement that replacing the hard drive would void the rest of the warranty.... only that the replacement or any damage caused by the replacement would not be covered.