Consider unbelievable versus its synonym incredible, and you will find what there is to be found of an answer here.
The general tendency is to use un‑ on Germanic words or any generic English term, and to use in‑ (possibly mutated; see next paragraph) for words of Latin origin. This is not hard and fast, however; there are of course exceptions.
Also, the Latinate in‑ prefix comes in other forms, like illegible, immutable, irreducible. Those also count as in‑ versions, not un‑ versions.
Similarly, ‑able is the more general ending, but -ible also frequently occurs. In fact, you will find that ‑able and ‑ance tend to go together, just as ‑ible and ‑ence tend to go together.
Here again there is an etymological explanation: whether it derived from either a Germanic word or from a first-conjugation Latin verb (so Germanic words or Latin ‑are verbs yield ‑able type endings) on the one hand, or whether it was instead from another Latin conjugation (so ‑ere verbs and such yield ‑ible type endings) on the other.
But as before, there are notable exceptions.
Vi is proper Latin, and it means "with violence, violently", the ablative of vis, "force, violence", from Proto-Indo-European *u̯i-, with similar meaning, and probably related to various other roots and their reflexes. Words like vir "man", virtus "might, virtue", violo "violate" (all senses) come from *vi-.
If you scribble v.c. next to your signature on a contract, it is said that you can thereby prove that you signed under duress, where v.c. stands for vi coactus, "coerced by violence". Presumably, illiterate criminals won't notice at the time of signing.
English vice and vicious come from Latin vitium "fault, vice", which comes from another, apparently unrelated Proto-Indo-European root *u̯i- meaning "apart, separate" (a vice may be errant from the right path?). This is probably related to evito "to avoid", related to English inevitable.
Best Answer
Most of them if they give an etymology.
Taking your examples, the OED gives:
The looking up capable
merriam-webster.com Gives:
Then looking up capable
So we can see, in‑ + (capere + ‑bilis) with ‑bilis / -abilis being the source of the ‑ble / ‑able suffixes.
Now, this does not break things down quite as neatly as in‑ + cap + ‑able, or even in‑ capere + ‑able but that's because the English word incapable is not in‑ + cap + ‑able.
Latin capabilis means comprehensible or intelligent, or being able to be received (in Christian theological use, God and specifically the Holy Spirit is described as capabilis).
This is not what the English word capable means, and nor did capere come into English with it. Hence not only is there no capere root (you suggest cap, but on what evidence?) in English, (the closest in English would be have and heave), but the English word capable does not mean the same thing as its source.
So while the dictionaries don't give as neat a breakdown as you ask for, that's because the reality they are describing does not have such a neat breakdown, and giving it would be an error.