Almost all knowledgable people linger in multiple groups, so you really should have posted this in the ePUB forum instead of the Sigil forum.
Now, with regards to your questions. The support of ligatures is dependent of the reader device. The older devices will not be able to handle it, since the ligature characters are not part of the font of the readers. The only way to have the ligatures in the old devices, is to embed a font with the ligatures.
That being said, the readers that support ligatures also have the tendency to create ligatures when the characters are next to each other. I believe the Sony does that and the reasoning is that it is better read experience for the reader. I think that for some readers you are able to turn it off.
Can you give cases where a ligature should not appear? If I recall correctly, it is only for certain languages like German. I think there lies the issue. The readers (and its software) are build in general for the English market (I know there are localized versions, but those are just translation). I do agree that the ZWNJ should be honored, but I am not too surprised it gets ignored actually... Have you tried with different embedding fonts like Charis SIL? You stand a good change ZWNJ is part of that font.
If the ZWNJ character is not part of the font (sounds silly since it is empty, but it needs to be defined), it will be ignored. Since on most readers the internal fonts are crippled/not complete, I would not be surprised if the ZWNJ is not part of it.
Last edited by Toxaris; 03-26-2013 at 04:20 AM.