Targeted genetic traits for plant nutrition can improve assimilation of N from air. See the paper "Impact of Genetically Modified Crops and Their Management on Soil Microbially Mediated Plant Nutrient Transformations" by P. P. Motavalli, R. J. Kremer, M. Fang, and N. E. Means (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.503.4674&rep=rep1&type=pdf.)
1. It depends on what kind of GM plants you have. If the transgenesis of your GM plants involve in 'overexpression' or ' knockout' of the nodule-specific genes encoded by the host plant, the so-called nodulin genes, you may get GM plants with abnormal nodule formation.
More info on nodulin genes: http://www.nature.com/nature/journal/v323/n6088/abs/323564a0.html
2. You may also un-purposely knock out an essential nodulin gene by genetically transforming of, for example, a GUS gene due to random insertion. This may also cause the abnormal formation of nodules.