哪儿 vs. 哪里, Difference in Meaning?
There's no difference in meaning. They are not actually all that distinct: both words came from 哪, a generic interrogative character used for indicating a question. Given an appropriate context (e.g. 在哪), the character expresses the meaning of "where". Both 哪儿 and 哪里 builds upon that.

The suffix 儿 is generally meaningless, and reflects the northern dialectical tendency for retroflex consonants. That is, when they say 在哪 it comes out sounding like 在哪儿, so you are essentially right about it just being a sound.

Southerners are less likely to curl their tongues like that, so 哪里 is a bit more common in the south. The second character 里 (裡) here means "a specific area of space". Combined the interrogative 哪, this readily becomes "where".