Is there a standard way of referencing line numbers in a draft?

Use whatever protocol you like, but explain your protocol to the editor and authors. For example, you could include something like the following (quoting from someone else's review of one of my own papers):

Throughout this review, "p.5(17)" refers to line 17 on page 5.

I'm not aware of a standard, but you can always define your own notation in your report. Perhaps some journals do have a recommended standard in their reviewer instructions, but I don't remember seeing that either.

If you want to go compact, I'd suggest "p1, R12" for page 1, right column (L for left), where 12 is understood to be the line number. That is, there are probably few enough columns that there isn't a need to have a running number for them...