Legitimacy, diplomatic sensibility, personal distaste towards Szapolyai, personal connections, prospect of easy manipulation of a childking, probably there are even more.
OP wrote, that Mary would be visibly pregnant by the time of Mohács already. If Louis II didn't question her, how could they?
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Rumours don't have to be logical all they need to do is to plant the seed of doubt for example although Mary is pregnant by the time of Mohács that does not necessarily mean that the child is Louis'... I'm thinking rumours such as Louis was perhaps incapable of fathering a child and not wanting to leave the throne vacant he would suffer the indignity of his wife having an extra marital arrangement and a voilà a male heir.
If the child is the unquestionable heir to the Throne i.e. his legitimacy is not in doubt then Ferdinand and János would not even be considered then maybe they would want to undermine the child king's claim and may concluded, separately of course, that if it is possible they would challenge the child's legitimacy and if the father is dead who would be around to say otherwise - Mary maybe but would anyone be that interested in hearing what she had to say.
My understand was that certain factions in the Hungarian Nobility favoured János whilst others favoured Ferdinand and that their respective supporters voted each of them to be King leading to the partition of the kingdom. János asked Süleyman I for help and correct me if I am wrong but Süleyman went and installed him in Buda. With Louis son out of the way János would be sitting pretty albeit as a vassal King to the Ottomans,
With all the Machiavellian plots swirling around the child king's head who would protect him? Would his mother have enough clout, being Austrian and the granddaughter of Maximilian I Holy Roman Emperor, or would her 'foreignness' be her downfall. Would Süleyman seek to manipulate the situation for himself - he may conclude that a true heir to the throne is better than a fake that owes his position to the untrustworthy Nobility, who seem to change their minds as quickly as the British weather, and therefore not all that reliable and more importantly he could use the child as a means to check the Habsburgs. As you say the prospect of easily manipulation could be very tempting...