I am interested in retracting my old journal articles. Would it have any negative effects on my academic career?
Yes, it would have severe negative effects. Don't do this.
Retraction is intended for two main types of situations:
The paper contains serious errors that completely invalidate its conclusions and can't be fixed just by publishing a correction.
The author is guilty of serious unethical behavior: plagiarism, fake data, mistreatment of animal subjects, studies on humans without their consent, etc.
As I understand it, 1 isn't applicable here: your results aren't false, they just don't go as far as they could. And the missing reference, especially if you didn't omit it intentionally, should be fixed by a correction or addendum. And 2 certainly isn't applicable.
However, if the paper is retracted, people will assume that it was retracted for one of the above reasons, either of which would be a serious black mark for a researcher. (You might like to browse http://retractionwatch.wordpress.com/ to see what kind of company you'd be keeping.) As such, it very well might completely destroy your chances of further academic study or employment.
Moreover, a retracted paper doesn't just drop out of sight. The publisher won't take it down from their website - they'll leave it there with a big RETRACTED stamped across it. It'll continue to be found in searches, and people who find it will assume that you're guilty of 1 or 2 above. Also, there's an argument to be made that ethically, you'd have to continue listing it on your CV, marked as "retracted".
(As others have mentioned, you don't have the right to retract a paper unilaterally. The journal has to make that call, and they should only do it if there's convincing evidence of 1 or 2 above. So the whole thing is probably moot. But even so, if you ask them to retract the paper, they're likely to think that you're confessing to 1 or 2, and you don't want to give that impression, even if it's cleared up before anything happens.)
The solution for having used low quality methods in the paper is just to do better work in the future. You could, if you want and as Buffy suggests, go back and study the same question with better methods. But I don't feel you're obligated to do that - if you are interested in other topics now, feel free to do that. People don't generally judge researchers harshly just because their early papers were less than outstanding. Indeed, the fact that a paper from a bachelors thesis got published at all will be a plus. In the long run, the focus will be: how good is your best recent work?
The solution for the missing reference is, as mentioned, to keep pushing the journal to print a correction or addendum. (If their editors were responsible for dropping the reference, they should admit that in the correction.) If they won't, you can post one on your own website.