Why do so many prefixes mean "Not"

Question

While trying to think of a brief list of English prefixes that mean "not" or "opposite to" in some way, I was wondering why so many exist.  As English has roots in so many languages, I was hoping somebody could help me understand maybe how some prefixes hail from different languages, and why we have kept all of them.  Perhaps there are micro-differences in meaning, and I'd love any insight on that. Examples of different prefixes all meaning the same thing, and examples, are below:

a- atypical
an- anaerobic
anti- anticlimactic, anti-clockwise (for Britons)
counter- counter-intuitive, counterclockwise
dis- disengage, disconnect
il- illegitimate
im- immeasurable
in- indestructible
ir- irresponsible
mis- misunderstand
non- nontraditional
un- unhappy

I know it's an antitypical question, but it's disunderstood in my head and seems misresponsible to have counterunderstood meanings to ameasurable words, making it unpossible for people to learn all these incommon prefixes.

Greybeard · Answer

The negative prefixes usually have a rather complex developmental history, and there is usually some overlap into similarly negative meanings. The following nuances can thus be considered as general, rather than specific.

•   a- atypical / an- anaerobic: These are the same - compare a cat/an egg. A-/an- =  without/ outside of / absent(prep.)
Compare amoral = outside the category of “moral”; that cannot be characterized as either morally good or bad. "Amoral" is basically neutral, (although when applied to human activity and because humans are expected to be moral) it is chiefly negative, and immoral -> contrary to “morals”: this is basically negative.

•   anti- anticlimactic, anti-clockwise (for Britons): anti+ X = in opposition to X/as opposed to X

•   counter- counter-intuitive, counter clockwise: in the opposite direction or sense, with a contrary effect, or in opposition, or response. From the adverb counter c1446   in T. Wright Political Poems & Songs (1859) II. 224   Now ye han founde parfite, love welle your game; For and ye renne countre thenne be ye to blame. (Now that you have perfection, love well the object of your pursuit; for, if [you do not] you will be running counter, and then you will be to blame.)  - Compare with contrary

•   de- des- di-, dif-, dir-, dis- disengage, disconnect – dis: to undo that which is already done or was the state/condition. ((i) disaster = dis + astra = against the stars -> ill-starred -> the undoing of [expected] fate. (ii)  Differ - Latin: dif- prefix + ferre to bear, carry.)

•   il-, im-, in-, ir-, ig-. These are all the same. = not. These are all related to “un-“

•   mis- misunderstand – this is the same “mis”- as in mistake = mistakenly; in error - both with a nuance of "unintentionally".

•   non- non-traditional = outside the category of (very similar to a-/an-)

•   un- unhappy = not.

A Koscianski · Answer

Here's what might be a piece of the puzzle. In the case of "i", it seems that words are modified to preserve pronunciation. This  happens in Portuguese; for instance, "legítimo / ilegítimo", "responsável / irresponsável": we get a double R because otherwise the result would sound weird.
This might be the case with the negation of 'responsible' and 'aerobic'.

Why do so many prefixes mean "Not"

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