Kushan's motives might be:
1) He hates Prateek for a long time due to his high-handed dictatorship over everyone in the company, he wanted to punish Prateek by kidnapping his daughter and now making him seem like the culprit.
2) Kushan hates Trisha too as she used to bully and tease Meghan. He also knew Bobby had a crush on Trisha and she was playing with both cousins' emotions. Hes punishing Trisha for all that as well.
Or
3) Kushan has always been BAD to the bone, he doesnt care abt anyone, not even for his kids, his sole motive for marrying Lavanya was to get loads of money and with Trisha he found that chance to hit the jackpot.
I dont think there was any affair between Trisha and Kushan, that would be really sick and unacceptable to desi viewers, so unlike the Spanish show they wont show this. I wonder how Lavanya and kids will react when they find out Kushan is the kidnapper.