Noggit doesn't render particle effects. Some (well, quite a lot of) models are made in fact only of particle emitters, which means that they have no part which might be shown in noggit.
There are 3 ways.:
1. use Clear models in Assist menu. That will, however, delete ALL models spawned on current ADT. And btw, it sometimes leaves 1 model undeleted, for unknown reasons to me.
2. extract m2 files of some model which is visible in noggit, rename them so their name match name of model which is giving you trouble and place them into you MPQ into directory where model, which you want to get deleted, belongs. This will rewrite particle-only model and change it to copy of original model. Which means that you will be able to see model in noggit - and delete it. Well, if there are a lot of such models, this will be quite a while to do.
3. delete models from structure of ADT by using another app, able to work with some kind of list of models spawned on ADT. Sadly, I am not sure if this is even possible and how to do it, if it is.