How to cite where names are not of [firstName lastName] form, in particular patronymic? In academia in the US, the dominant name format is [firstName lastName]. And in APA citation format you typically cite by referring to the last name. So e.g. if John Doe wrote a paper in 2014, you might cite it as Doe (2014).

More generally you'd cite by referring to the family name. So e.g. if the Chinese basketball player Yao Ming wrote a paper in 2014, you would cite it as Yao (2014), since Yao is his family name and Ming is his given name. But there is typically no confusion anyway, because when East Asians publish in Western academia, they simply give in to Western convention and reverse the order of their names. So Yao Ming would typically simply have his name printed as  Ming Yao. And so we're back to the [firstName lastName] format and there is no confusion.

My question is: What about patronymics? E.g. if Osama bin Laden writes a paper in 2014, should he be cited as Osama (2014) or bin Laden (2014)? It seems that unlike with East Asians, people with patronymic names have been less inclined to give in to Western convention and reverse the order of their names. So his name would still appear as Osama bin Laden  on the title page. 

Suppose I notice that everyone simply cites his paper as bin Laden (2014). (Indeed, in the real world, this is how Western media outlets often refer to this historical figure, even though this makes as much sense as referring to George W. Bush as simply George.) If I want to cite this paper, should I simply follow what is now the convention and cite it as bin Laden (2014), even though this is mistaken? Or should I cite it as Osama (2014), at the risk of my peers having no idea which paper I am talking about? What is or should be the proper convention?

Note that this 'problem' is not limited to Muslim names. Even in Europe there are e.g. Icelandic names. There are also some cultures where people go by a single given name (i.e. no last name/family name/surname) but which may sometimes be composed of more than one word (e.g. sometimes in Mongolia, Burma, South India, Indonesia).
Interesting question. The best thing would certainly be to consult the journal's style manual or, if this does not yield an answer (as is likely), to ask the editor. Their response is conclusive. Having said that, the issue seems to be very complex. There are no hard and fast rules. I quote from the "Referencing Manual For IAIS students" (Arab and Islamic Studies, University of Exter):


  Some names are made up of fifteen or even twenty words, and it can be
  baffling at first glance to determine how to put the various elements
  in the right order. […] Any one of these elements can become the 'urf'
  (customary name).
  
  […] 
  
  Once you have established the ‘urf, it is customary to follow this by
  the author’s given name (ism) and the name of his father (nasab)
  joined by the word ibn (son of – also written bin) or bint (daughter
  of) in the case of a woman.
  
  […]
  
  Surnames are a relatively recent phenomenon across the Islamic world
  and modern Arabic names only came into existence towards the end of
  the 19th century. It is now accepted practice, particularly in the
  West, to treat the final element of a person’s name as a surname and
  the first as a forename, so it is now correct to cite Taha Ḥusayn as
  Ḥusayn, Taha, although you will find Taha Husayn in older books and
  catalogues. The Western obsession with the surname can lead to some
  strange coinages, for example Saddam Hussein’s full name is Ṣaddām
  ibn Ḥusayn al-Tikrītī, yet it is now standard to cite him by his
  father’s given name (Ḥusayn) as a surname. (Most second forenames
  indicate the father’s name, which is why names such as Aḥmad can be
  found as the second element in women’s forenames). Similarly, the form
  of given name `Abd (slave/servant of), followed by one of the
  ninety-nine names of God, should never be split from the element which
  follows it, although most Westerners still cite Jamāl ‘Abd al-Nāṣir
  (wrongly) as Nasser.


The referencing manual suggests to use the following established bibliographic resources to find the 'urf (customary name):


the bibliography of a scholarly book (however, different sources will quote the same Arabic name in different ways)
the Exeter University Library catalogue, which uses the best-known name in the Library of Congress transliteration
the Encyclopaedia of Islam
the Library of Congress Authority List


In all of these cases, problems with transliteration may render it difficult to look up the proper name.

The University of Malaya's APA Formatting and Style Guide is another useful resource.