Learn Finnish: Onko tuo reikä leivässä? - Is that hole in the bread?

This is consonant gradation! When we add the inessive ending -ssä (in), it closes the final syllable. This forces the strong consonant p in leipä to change to the weak consonant v, making it leivässä.

Why does the word reikä keep its "k" here? Doesn't "k" normally disappear in consonant gradation?

It keeps its k because reikä (hole) is in its basic dictionary form here. Consonant gradation usually only happens when we add an ending to a word. Since we haven't added any grammatical endings to reikä, it stays strong.

Why did we add -ssä to the end of the bread instead of -ssa?

This is a quick reminder of vowel harmony. The word leipä has the front vowels e and ä. Finnish rules say we cannot mix those with back vowels like a, so we must use the front-vowel version of the "in" ending, which is -ssä.

How exactly does onko make this a question?

The word on simply means "is". When you want to ask a yes/no question, you attach the question particle -ko (or -kö) to the verb and move it to the front of the sentence.