Should I use double quotes throughout the paper even after defining the terms in the introductory section?

The usual convention in CS:

• Use italics when you first mention the term and define it.
• After that, you will use it just like any other word. No italics, no boldface, no quotation marks.

I think it would be unusual to do that, actually. However, if you want to "emphasize" the terms at each use you could use some typographic form. I would suggest italic, however, over double quotes. Imagine a CS paper in which every use of "list" was printed that way.

But using a typographic convention should really only be needed if the word defined is also a common word or term that is also used in its normal sense in the paper as well as its newly defined technical sense.

If you over use typographic conventions, by the way, say, ALL CAPS and bold and such throughout a paper without a good reason, the paper just starts to look ugly and will be harder to read. The reason I suggest italic above is that it is easier on the eye.