To me using the phrase niggling is no different to me saying "chink in the armour" about an East Asian person. The phrase by itself is not racist nor does it have racist origin but when you think of the context of which it was used it is inappropriate, rude, racist. This phrase would never have been used by the likes of the Telegraph / Times despite being right leaning papers like the Mail as they would know that their readers would understand the hidden meaning of the words. The daily mail readers are either too stupid to see the hidden meaning or knew the meaning and just didn't care as they believe the diatribe the Mail give them about meghan.
If you believe no one in the DM press room who read the article before going to press knew about the second meaning (journalists who have studied at oxbridge and attended elite public schools studying the english language and the eytomology of words from Latin, french etc), you are either naive, disingenuous or both.
There are so many things the press could say about meghan without the passive aggressive references about her heritage. By doing this, it negates any genuine critiques they have made about her.