If Shankara considered Nirguna Brahman superior, or in other words, if he was a promoter of Nirguna Brahman, then why did he mention the name of Narayana (as his ishta devata) in the introduction of his Bhagavad Gita commentary (Gita Bhashya)?
According to Sankara there is only Nirguna Brahman. There is strictly speaking no Saguna Brahman.
Brahman is only formless to be sure, for that is the dominant note (of the Upanishadic teaching).
"For that is the dominant teaching", inasmuch as it has been established under the aphorism, "But that Brahman is known from the Upanishads, because of their being connected with Brahman as their main import" (I.i.4), that the texts like the following have for their main purport the transcenddental Brahman which is the Self, and not any subject matter: "It is neither gross, nor minute, neither short, nor long" (Br. III.viii.8), "Soundless, touchless, colourless, undiminishing" (Ka I.iii.15) .... and so on. Hence in sentences of this kind, the formless Brahman alone, just as It is spoken by the texts themselves, has to be accepted. But the other texts, speaking of Brahman with form, have the injunctions about meditations as their main objectives. So long as they do not lead to contradiction, their apparent meanings should be accepted. But when they involve a contradiction, the principle to be followed for deciding one of the other is that, those that have the formless Brahman as their main purport are more authoritative than the others which have not that as their main purport. It is according to this that one is driven to the conclusion that Brahman is formless and not its opposite, though texts having both the purports are in evidence.
Brahma Sutra Bhasya of Sri Sankaracharya III.ii.14 translated by Swami Gambhirananda
Why does Sankara write hymns of Saguna Brahman and as mentioned in the question refers to Narayana in the Gita bhasya?
Sri Sankaracharya wrote these hymns to help those who follow the path of krama mukti or gradual liberation by stages.
(The journey of the souls along the path of the gods is) not restricted (to any particular meditation). It applies to all meditations (on the qualified Brahman). This involves no contradiction as is known from Upanishadic and Smriti texts (lit. direct text and inference).
Vedantin: This being the position, the aphorist says, “There is no restriction” etc. The path of the gods should pertain to all the meditations on the qualified Brahman, calculated as they are to lead to good fortune (i.e. Brahmaloka).
Brahma Sutra Bhasya of Sri Sankaracharya III.iii.31 translated by Swami Gambhirananda
What happens to those who succeed in reaching Brahmaloka by meditation on qualified Brahman or Saguna Brahman?
On the final dissolution of the world of the conditioned Brahman, they attain, along with the lord of the world, what is higher than the conditioned Brahman, as is known on the strength of the Upanishadic declaration.
The idea conveyed is that when the time for the final dissolution of the world of the inferior Brahman is imminent, the aspirants who have acquired full realization there itself attain, thereafter, along with Hiranyagarbha, the ruler of that world, the supreme state of Vishnu which is absolutely pure. This kind of liberation by stages has to be admitted on the strength of the Upanishadic texts speaking of non-return etc. For we established earlier that it is incomprehensible that the supreme Brahman should be reached by any process of moving forward.
Brahma Sutra Bhasya of Sri Sankaracharya IV.III.10 translated by Swami Gambhirananda
Sri Sankaracharya admits that liberation by stages or krama mukti is possible though he recommends pure Jnana Yoga. The path of krama mukti is for those who are for different reasons incapable of doing Jnana Yoga.
Sankara's acceptance of Saguna Brahman from the practical point of view while denying it's existence from the theoretical point of view made Vaishnava Acharyas call him Pracanna Bouddha.