What does "Inahent the coonter she's no' near sic a nochtie, shilpit, wee thingie" mean?

You can use the Online Scots Dictionary for a lexical translation. Entering your sample text yields these definitions:

inahent = in ahint: ...in behind.

coonter: A counter.

no' = no [no:, na, N. ne:]
adv. Negating a v., adj. or adv. Not.

sic a: Such a.

nochtie [noxti]
adj. Good for nothing, insignificant.

shilpit ['ʃɪlpɪt]
also shilpin ['ʃɪlpən]
adj. Pale, sickly, weak, puny, shrunken.

wee [wi:]
....
adj. Small, tiny, little, restricted in size.

thingie = thing [θɪŋ, hɪŋ, hɪn, I.Sh. tɪŋ]
n. A thing. Kind, sort, stuff. Reason, cause. Amount, quantity, number, extent, cost. pl. things.
dim. thingie, thingmie, thingum

So, yes, your translation is 'correct', but I don't think it entirely catches the spirit of the thingie. I would translate it as

Behind the counter she's not such an insignificant, puny, tiny little thing.

It's an understatement to say we're talking about somebody who's not small behind that counter.