.ctk files are OK, they're used for changed block tracking and allow the backup software to back-up only the blocks that have changed since last backup (incremental) instead of copying full vmdk every time.
What you should probably worry about is the number and sizes of 00000*.vmdk files. Those actually are your snapshot data. VMware recommends that for production the average snapshot life cycle should not be longer than few hours, max 1-3 days in some cases. But essentially you want to make it dissappear as soon as you can.
There will be disk IO performance impact on VM that has snapshots, especially during write operations. Basically every virtual disk IO that your guest issues can result in multiple physical disk IOs (AFAIR if VM wants to change a block that already exists somewhere up the chain, the block is first copied to current delta and only then vmkernel does the write, so it's 1 Read + 2 Writes instead of just 1 Write IO) so you're essentially doubling or tripling your disk load, queues fill up, so does the latency and VMs are getting "slow".
Snapshot delete or consolidate operation is an extremely disk-intensive process which is why your'e seeing performance drops. The bigger the snapshot, the more data needs to be copied from deltas to base vmdks and since your disk spindles can produce only as much IO as they can, the operation takes longer and you're starting to notice the impact.
Basically it should be so that most of the time your VM has no snapshots at all, backup process kicks in and creates one, then does the backup and cleans up the snapshot afterwards. I would probably start with determining why the backup software does not clean up after backup job has finished. Involve your backup vendor's support if you can. This is a quite popular problem with backup products, those guys are solving hundreds of cases like this on daily basis so most probably your vendor will have a quick solution.
Snapshotting is a great feature if used appropriately (life cycle for a running prod VM snapshot ideally limited to few hours max) however it can do a lot of harm if you misuse it or leave your snapshots unattended (including data loss).
Hope this helps.