Sorry nobody replied in so long, but yes, water will find a way through. There is no way I know of to stitch clay to a liner and hope water doesn’t leak at the junction of the two. It will. Rubber liners are all or nothing.

You do need to install them properly, and I don’t think a steep side will work well, so you may need reshaping so that the liner can be buried without materials sliding off of it. In smaller ponds you can staircase the slopes, and pin the liner with a layer of felt to prevent puncturing, and large rocks on the felt. A larger pond would be a big project to do this. The staircase will require a bit more liner, but has a lot of benefit to it for getting in and out as well as preventing materials from sliding. Also a place where plants in containers can be placed like lilies.

First I would try to drain it down in your dry season and leave enough water for the fish, and address the areas where you have erosion issues. Bring in some good clay, stir in some soilfloc, and compact it down in the suspect areas. Then place erosion control netting on top. Seed it with rye grass or similar to help hold it together. Pray for appropriately timed rain for a refill.