Shahrukh Khan and Kader Khan never worked together. Kader Khan had a cameo in “Oh Darling Yeh Hai India”, as one of the bidders.
Though they were in the same location for a scene they did not had a dialogue exchange.
The main reason for their non-collabration was that their peak careers didn't perfectly overlap. During the initial stages, Shahrukh gained fame as an anti-hero followed by a romantic hero. At that time Kader Khan had just stepped out from villainous roles and was on his comedy streak especially with Govinda and David Dhawan.
Besides this, their preferred teams were different too. Kader Khan worked extensively with David Dhavan at that time while Shahrukh’s major collabrations were with Yash Chopra and Karan Johar.
Post - 2000s Kader Khan also had significant health issues which was later followed with a knee operation and wheel chair dependency which limited his participation in films.
So there was no professional conflicts between the two. The main reasons for their non-collabration was differences in their career timelines, lack of suitable opportunities and natural divergence of their individual film trajectories.