Will I lose Aperture by upgrading from OS X 10.8.5 to El Capitan?

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Yes but, I have no idea how long for, the next update may break it.

If I update to El Capitan… will I be able to continue use of Aperture 3.4.5 for photo editing?

No, Aperture 3.4.5 will not run in El Capitan. You will need Aperture 3.6 for El Capitan.

Follow the link provided by Niel for how to proceed.

There are more and more issues with Aperture. It is running on El Capitan, but the minor bugs keep accumulating.

• When brushing adjustments, the position is slightly off.
• The thumbnails in list view are upside down. Re: Aperture and El Capitan OSX
• If you add a Curves adjustment the straighten adjustment will not be visible in the exported images. See: straight
• The link to the plug-in page does no longer work.plugins

And you can no longer order print products from Aperture. Apple stopped the support for Print products from aperture completely.