You are writing a thesis in computer science.

I can use my own personal experience as a guide in answering your question. Rarely, if ever, have I seen symbol repetition in a single college textbook on anything science/math related. However, across different subject matter and their associated different textbooks we do see symbol repetition. A college textbook on calculus might very well use similar symbols as a college textbook on physics.

Your thesis will get confusing if you use X for this and X for that in a single thesis. In my estimation, you have to come up with a way to clearly convey the differences to the readers. You shouldn't confuse the readers in your thesis. It's counter to conveying the fact that you have a mastery of your subject matter. All that being said, I don't think it will be difficult to differentiate all of your symbols. There are many different combinations you can use to convey differences consistently through your thesis.

**********************************

This may be a longshot suggestion, but perhaps you could start incorporating symbols from your computer's "Character Map" GUI. For example: **Ǟ ź Ǥ**

Those three are all from the Arial selection from "Character Map". There are many others.

********************************

I don't see any problem whatsoever with re-using a symbol that represents the same thing throughout your thesis. That is done everywhere and in every college textbook I've ever seen. For example, if $_rho$ means density throughout the thesis then you should be able to use it whenever density is discussed.