Is the UI in 2.9 customizable? I just saw 2.5 UI and it does look more organized.
It is. It can not however be used to model for Morrowind. You could create you model in 2.9 save it as a blender file, load it into blender 2.4.9 and then export it to .nif format. But only if you do not use any of the features of 2.9 that are not available in 2.4.9. It is much easier to simply use 2.4.9 as that is the latest version with a working exporter.
Although 2.9 has additional options available and a nicer interface those options do no benifit in that they are not supported by the Morrowind game engine. Version 2.9 is a great 3d modeling package so it is well worth getting if you do any modeling outside of Morrowind moding.