There's quite a lot more to this than these two words. Ripple and cripple are both English Simplex Words. Those include all the monosyllables, and also monosyllables with one of a list of extra "half-syllable" suffixes, of which syllabic /ḷ/ is one. Most simplex words -- more than half, by our count -- have sound-symbolic associations that go along with their pronunciation.
Phonosemantically, the important things are the initial Assonance or consonant cluster (respectively /r-/ and /kr-/ here), and the Rime /-ɪp/. The rime is extremely salient. The assonance /r-/ doesn't have much significance -- there are too many words beginning with it -- but the /kr-/ assonance is very salient, too.
Essentially, simplex words with the -ip rime refer (somehow) to something with a 3-dimensional part and a 2-dimensional part, which matches both a cripple and a ripple. Cripples are solid, but they were distinguished in English as people who can't walk; prototypically they must crawl (there's another kr-, btw), on a 2-D surface; and ripples are a 3-D feature on a 2-D surface.
The kr- assonance is also dimensional, and refers to 1-dimensional split or bent things, many of which are compressed or shrunken. It's easy to see why cripple and crutch and crouch go together.
So the assonance and the rime are coherent, which happens a lot. Like clump, as in a clump of trees; kl- means together, while -ump means a 3-dimensional solid, roughly the same in all dimensions. So what's a clump of something? It's a group of trees, or cells, or something else, shaped like an -ump.
Though the system handles contradictions nicely, too: st- refers to vertical rigid 1-dimensional things like sticks and storks and stacks, whereas -ump is round like bumps and lumps and humps. So what's a stump? It's something that used to be tall and 1-dimensional, but is now an -ump.
More information on phonosemantics (for those who can stand it) is available here.