From the Wikipedia article, the Large and Small Magellanic Clouds were observed prior to Magellan's expedition, and the name only stuck long after Magellan's expedition (at first, they were called nubecula major and nubecula minor, or Large Cloud and Small Cloud). So why were they finally named after Magellan?
Michel Dennefeld has written an arXiv paper, "A history of the Magellanic Clouds and the European exploration of the Southern Hemisphere" which goes into the history of the European discovery of the Magellanic Clouds and the history of the name. The term Magellanic clouds appears to have originated with sailors, as noted by Edmond Halley in his 1679 "Catalogus Stellarum Australium":
His work is known because of the inclusion of a new (fleeting) constellation, Robur Carolinum, to please King Charles II. He mentions in an appendix that:
Proxima, ex iis quas observavi, est in Cauda Apodis, in distancia paulo ultra 8 graduum, Duae Nubeculae, quae a Nautis Nebulae Magellanicae appellantur, exacte referent Galaxiae albedinem & Telescopio inspectae, hinc inde Nebulas Parvas & exiguas Stellas ostendunt…
It appears it was clear to him that the name Magellanic Clouds was used only by sailors, and that those Clouds resemble the Milky Way.
Dennefeld goes on to describe the gradual spread of the term "Magellanic Clouds" beyond the nautical community, e.g. in Nicolas de La Caille's 1755 catalogue:
But his words, “que nous appelons nuées de Magellan”, seem to indicate that around that time the association of the Clouds with Magellan was already spreading beyond the nautical community, even if the scientific term was still simply Nubeculae or les Nuages.
The astronomical usage switched from "Nubeculae" around the time that Latin was abandoned as the language of science, and the first usage in the scientific literature seems to have been by John Herschel:
John Herschel (1847), in a section however entitled "On the two nubeculae or Magellanic Clouds", talks only about Nubeculae. Only in the accompanying figure (Fig. 8), where he gives his visual observations (figure where it is however hard to recognise the Clouds), does he mention again, "The two Magellanic Clouds as seen with the naked Eye". So he uses both the scientific denomination and the more public name, and Herschel seems to have been the first one to use the name Magellanic Clouds in a scientific publication.
So it appears to be that the name became Magellanic Clouds because this is the name that was originally used by European sailors, that then gradually became the common name as Latin was abandoned.