For the books, GRRM's line was that Aegon 'set out' to conquer the Seven Kingdoms that exists on Westeros at that time: the North, Vale, Westerlands, Stormlands, Iron Islands/Riverlands, Reach and Dorne. And that's the source of the term 'Seven Kingdoms'.

So in overall terms, the fact that the Targaryens failed to conquer Dorne (first time around, anyway) is irrelevant. They still claimed to rule it, even if it was 200 years before this became a reality.

However, some people don't like the idea because that suggests that the Isles and Riverlands were still one polity under the Targaryens, when of course they were not. The Isles were ruled by the Greyjoys from Pyke and the Riverlands from Riverrun by the Tullys. So fans have rationalised it that the 'Seven Kingdoms' split the Iron Islands and Riverlands and didn't include Dorne. When Dorne joined, the Iron Islands appear to have been in a state of rebellion (between the First Blackfyre Rebellion and after the Great Spring Sickness they were reaving the coastlands), so fans rationalise that the Iron Islands were dropped from the count and replaced by Dorne. Though the Iron Islands were still a semi-autonomous region, they weren't included in the count. This is backed up by the goblet Joffrey gets from the Tyrells, and his suggestion they should re-promote the Iron Islands after their conquest of Winterfell.

GRRM's only comment on the matter has been something along the lines that it's an argument that trainee maesters get worked up over in the pub, but no-one else really gives a toss. The realm is called 'The Seven Kingdoms' but there's actually eight Great Houses and nine administrative regions (or ten, if you count Dragonstone separately to King's Landing). That's just how they roll.

In the TV series, they seem to be rather more pedantic. It is the Riverlands which is counted as a semi-autonomous region like any of the others, but they are not counted as one of the Seven due to them not having had a king for centuries when the Targs invaded. In every other respect they're the same. This is backed up by a further line in Episode 7 which even suggests that before Dorne joined they were called 'the Six Kingdoms'. Which is a weird way of going about it, but more power to them. Of course, what is said on the TV show has no bearing on the books at all.