Key Prefix KDF with Counter I don't want to discuss the security problem with MD-based hashfunctions when using them as KDF. Since the existence of SHA3 or Skein hashfunction it is possible to use them as key prefix KDF.

What I mean with key prefix KDF is the following:
In https://eprint.iacr.org/2010/264.pdf you can find it or in short:

KDF(x) = H(x||1)||H(x||2)||...||H(x||n)

H is a Hashfunction, x the seed, the numbers are a counter.
While it is not specified what the counter is exactly is, I have a question.
The Counter starts with 1 and goes to N. How many Bytes is that Counter? Is it a single Byte?
I think you're encountering the difference between an academic paper and an implementable standard like an RFC or NIST Special Publication.

In an academic setting, details like encodings rarely matter. Using a uint8, uint16, or plain old int results in the same security in this case. So the counter can be encoded however you wish. 

However, unless you foresee a true need to generate enormous outputs, I would use a single byte and ensure that you return an error if the requested output is larger than 255*(hash length). This prevents the user from mis-using your KDF in an application for which it was not designed.