I thought the subject of the sentences is "colour" and not "pencils" so that verb to be should be in its singular form "is".The reply to the above sentence " what colour....." could be :
"The colour of my pencils is blue"

The scence behind the original question might be there are a batch of pencils of the same colour and so the original question comes out to be "what colour......" and not "what colours....".

If the scence behind the original question is that there is a batch of pencils of different colours, the question will then come come out to be "what colours.....", but this is not the original question. The reply to the question asking "what colours ......." could possibly receive a reply of:
"The colours of my pencils are red and blue."

I am still a bit confused and hope to be enlightened.

Thanks,
Tom Tong