Is it necessary to deglaze the cylinder tube and how do you do it?

While it's not always necessary, it's usually a good idea. After long periods in service, the internal surface of cylinder tubes can actually become too smooth. As a result, the replacement seals may leak.

Deglazing/deburring also removes spot rust and other minor surface imperfections - which is essential for optimum seal life.

The tool that's most often used for this job is a Flex-Hone. The correct technique for using one is shown in the video "How to Use a Flex-Hone":

http://www.brushresearch.com/videos.php

If your going to try to repair your hydraulic cylinders, it's well worth three minutes of your time.