This may be utterly unsatisfactory, but I think the right answer is, very Dutch, it mostly doesn't matter.
In regular body text, the difference is so subtle that the average Dutch person will not notice. I am a native Dutch, and quite a language and typography nerd besides. I had to look real closely at your example to see what you were asking. Neither example strikes me as explicitly right or wrong. Number 2 bugs me a bit because the kerning for Courier is off here--too tight around the ligature. Comes with being a monospace, I suppose.
This wouldn't be Dutch or language if there weren't exceptions. If IJ is capitalised (as it should, never capitalise only the I), it is usually displayed as a ligature. If the text is in all-caps, it's up to the typesetter. If the text has a large tracking value, don't use the ligature; split up the i and j in that case.
Another important exception where it does matter is when a word contains the ij substring, but it is not used as the 'long i' the ij diphthong represents. Examples would be 'bijection' (from your other question) or 'bijoux'. In these cases, never use a ligature. There are hilarious examples of Dutch incorrectly using Y as a replacement for IJ and spelling 'bijoux' in allcaps as 'BYOUX'.
A small correction: ij or IJ is never considered a single letter in Dutch. It may be represented by a ligature (or something that closely resembles one) in both upper- and lowercase, but it is still two separate letters.
Case in point: Dutch Scrabble and Wordfeud have I, J and Y as tiles, and not an IJ tile. Words with IJ have to be constructed with an I and a J tile. Dutch keyboards have no IJ key and, even as a native Dutch, I can't for the life of me remember the last time I used an Alt or keyboard code to output the ASCII ligature