We are currently performing peoplesoft application upgrade i.e,moving from Peopletools 8.49 and HCM9.0 TO Peopletools 8.52 and HCM9,1 FP2.
My doubt is that will all the MP's and Bundles applied in Source DB be moved to Target DB after our upgrade process.
FP2 will have the MPs in it. And yes, the upgrade process will move all of them to your target db.
There is a separate certified upgrade path HCM9.0 to HCM9.1 FP2. Use the template and documentation from this.
Check this old post in the forum - https://forums.oracle.com/thread/2427510
Hope this helps