do they need to account for them? I mean “nationalism and religion are bad” would seem to be sufficient.
You kind of do need to account for them if you have a central premise like “all conflict is class conflict.”
An easy out is to say that nationalism and religion are forces that enable you to mobilise people to engage in war against their class interests, eg. convince workers that they are German and that they should go and fight for German bosses against the French workers instead of uniting and deposing the bosses.
Maybe the next question is why people find nationalism and religious belief so much more appealing than class consciousness, and the answers to that are fairly obvious and explain why international socialism has been on the back foot since 1914.
Communist: Workers of the world, unite! Abandon your culture and possessions to pay into an enormous and anonymous group which will eventually be defined by the entirety of humanity!
Nationalist: The nation is my extended(2) family, its culture is my culture, its glory is my glory, its benefit is my benefit.
I’m going to be a bit uncharitable here - Communism appears to be rather hollow and unsatisfying to humans compared to religion and nationalism, and I’m not even religious. It leaves substantial corruption in its wake, and I can’t help but wonder how China would be functioning now if they didn’t try to get rid of the old culture.