Should tone sandhi be written in pinyin? Tone sandhi is a phonological change occurring in tonal languages, in
  which the tones assigned to individual words or morphemes change based
  on the pronunciation of adjacent words or morphemes.


For example 不是:


the original tone for each character is: bù shì (4 4)
After tone sandhi: bú shì (2 4)


Some say that it can be confusing to write it as if it is written, it would be confusing to know what the original tone is supposed to be.

Is there an standard practice to address this?
Tone Sandi rule should merely apply to spoken. In written, you should always put original tones in any forms of exams except that those exams are testing the rule itself. 

In fact, I doubt most of natives are aware of the existence of Tone Sandi indeed. But they do apply the rule naturally in practice. I suggest you study by phrase, not by character. That way you will know how each character will be used and the way to pronounce in practice.