There's no strong reason not to make version nullable.

The weak reason is that with text-like fields both '' (empty string) and null (null) might be valid values with different meanings, and making text-like fields non-nullable when they aren't meaningful may slightly reduces potential confusion in the future -- you don't have to go check if null and '' mean different things or not. With PHIDs, '' is consistently never valid so there isn't as much of an ambiguity. But I don't think it's really ambiguous here, and EditEngine has reduced how much of a problem this is by getting rid of all the if ($old === null) { ... } stuff around creation transactions, which was the major case where null and '' meant different things.