IF you did not buy Aperture from the AppStore but the boxed retail version, you may not see the Aperture update at the AppStore.
Then give the App Store Support a call.
The update to Aperture 3.6 can only be installed from the App Store. but if you bought a boxed retail version, your copy is not associated with your AppleID and you cannot update directly. Ask the AppStore Support for a redeem code, so you can purchase the update for free. Other forums members had success. You will need to provide a proof op purchase of Aperture and insist to talk to the manager.
Use this link: http://www.apple.com/support/mac/app-store/contact/
Apple sent redeem codes for Aperture 3.6 to several users who had bought the version on disks, if they could provide a serial number, so they could download the update for free. See for example this discussion: (The post marked as the solution)
Re: Aperture update not possible after update to Yosemite
It is really unfortunate you missed the window of opportunity with Mavericks MacOS X 10.9.5, when the update was easy.