Well, it does use NTFS instead of ext2/ext3, ReiserFS, or whatever. What do you mean "destroys"? Do you mean that they get obliterated upon installation? That in itself, I doubt, is true.
It is true that Vista will install its own bootloader which will prevent you from booting Linux, but that is easily remedied by reinstalling the other bootloader you had e.g. GRUB or LILO. For this reason alone it is best to install Windows first if you wish to have a multiboot system, as you install Linux/other OS next and the custom bootloader will overwrite the Microsoft original. This will avoid you a headache as setting up a bootloader manually is a complete pain which is often avoidable.
vista will only format the partitions you tell it to, so as long as you install it on a diff partition to linux then it will be ok.
although you will need to fix the boot loader like said above ^
ive never had to do this though as ive always installed windows first