As with most questions regarding the motives of Egyptian rulers, the simple answer is that we don’t know for certain: Egyptian kings in their inscriptions rarely wrote down their thought-processes for doing anything, beyond “it’s what the god would want”. There are a few exceptions (e.g. in Thutmose III’s Annals, and Ramesses II’s Qadesh texts), but those are extraordinary works in many ways, and in this case really the exceptions that prove the rule.

As you note, taking and counting the phalli of enemy soldiers after battle was not the usual Egyptian way for recording the scale of their victories and how well individual soldiers had fought: this was typically done by cutting off hands and presenting them to the king/royal herald, and this was so ingrained as a practice that ‘to take a hand’ was an idiom used by non-royal Egyptians for ‘to kill’, in order to reserve the actual act of killing enemy soldiers for the king. Nevertheless, castration of the enemy is attested (symbolically, if not in practice) at the beginning of pharaonic history, on the Narmer palette, so Merenptah is not necessarily innovating greatly in this respect. Ideas of feminisation and virility play a particularly pronounced role in Merenptah’s ideology in general (and Ramesses III’s as well, probably modelled to some extent on Merenptah’s). So we get in the Athribis Stela (V2) ‘the Nine Bows are before him like the women of the court’), Triumph Stela (6-7) ‘the vile, enemy chief of Libya fled in the depths of the night, all alone, no plume on his head, his feet bare; his wives were taken before his face’, (27-8) ‘Hurru has become a widow because of Egypt’. So mentioning the taking and counting of the enemy phalluses plays a part in Merenptah’s broader ideology as king; also, Merenptah’s victory was not a foreign conquest (like earlier kings) but a defence of Egypt from invaders, so there was perhaps a greater need for ideological retribution.

As for why they counted circumcised and uncircumcised phalluses in the first place? It had been thought that this was related to ideas of purity and cleanliness regarding circumcision, based on a bit of Herodotus (2.37), and a possible misreading of Piye’s stela (150-1); the evidence both of these provide is now viewed as a bit suspect and at any rate around 600 years after Merenptah, so not necessarily relevant. In fact the reason for cutting off and counting the phalluses (and specifying whether they were circumcised or uncircumcised) was probably fairly simple: it made it easier to count the different ethnic groups that made up the enemy army, and the Egyptians really liked listing things and counting, which helps to explain why the Egyptians counted both the hands and phalluses in this instance. This combination of ideological and bureaucratic reasons is nicely seen in Merenptah’s Great Libyan War Inscription (l.46), describing the bringing of the captives back to the king: ‘donkeys before them, laden with uncircumcised penises of the Land of Libya, with the hands of [every] foreign land which was with them, as fish in baskets’.

Secondary References

O’Connor, D. (2005), ‘The Eastern High Gate: Sexualized Architecture at Medinet Habu?’, in Jánosi, P. (ed.) (2005), Structure and Significance: Thoughts on Ancient Egyptian Architecture (Wien): 439-54

Quack, J. F. (2013), ‘Conceptions of Purity in Egyptian Religion’, in Frevel, C. & Nihan, C. (eds.) (2013), Purity and the Forming of Religious Traditions in the Ancient Mediterranean World and Ancient Judaism (Leiden): 115-58

Matić, U. (2019), Body and Frames of War in New Kingdom Egypt: Violent Treatment of Enemies and Prisoners, Philippika 134 (Wiesbaden)

Matić, U. (2021), ‘Gender-Based Violence’, in Wendrich, W. (ed.), UCLA Encyclopedia of Egyptology (Los Angeles)