It can. That's the problem. Kde kupujete vajíčka. is most likely the most common word order. But the 'kde' at the end is totally possible. It emphasizes that you want to know where they buy them. Which may sound silly, since the original question is also about where.... But you can do the same in English. "and you buy those eggs where?"
Can I in the written form distinguish this question from "Where are you buying eggs?" as opposed to "Where do you buy eggs?" There is enough nuance in English to consider them not completely equivalent. Is it the same in Czech? Is syntax completely irrelevant in Czech? Does it just depend on intonation and context?
The syntax is flexible, yet, different word orders may put emphasis on what it is we are the most interested in in that question.
I. e. KDE KUPUJETE VEJCE?. this is completely neutral question. We are simply asking where you buy egss.
KDE VY KUPUJETE VEJCE? i am interested particularly where YOU buy eggs. I have just told you I buy them in Tesco and I want to know where you go for them.
VEJCE KUPUJETE KDE? I am particularly interested where you buy EGGS. I do not care where you buy milk or bread.
Answer to all 3 question is the same. Walmart....
And a lot can be said by emphasis. Which I am not able to put on paper.
Difference between "buying" and "buy" is likely even more nuanced in Czech (in this particular case).
Buying = kupujete buy = nakupujete