Ok, if you were never asked to sign an inventory either when you first moved in or when you re-signed the tenancy then the Agents/landlord would find it very difficult if not impossible to show what damage had been done by you. This is really the fault of the Agent, nothing to do with you.
You can either state upfront to the Agent that, as you have never seen an inventory, you expect no deductions from your deposit.
Alternatively, you could wait until the check out is done and then, if there are deductions which you think are unfair, you can demand the return of any deposit withheld with the threat of going to the Small Claims Court if the Agent didn't comply.
Speaking as a landlord, I would hope that you were honest about it and pay for any damage (fair wear and tear excepted) that you caused but this is really the Agent's fault from what you say.
Is your deposit protected in a Scheme, or was it taken before the Schemes came in?
As to your first question, it's not a 'legal' right to be present at the check out but it would certainly be best practice on behalf of the Agent or Inventory Clerk for you to be present and nearly all of them would expect you to be. Of course, if you are there and they pull out an inventory to check you can simply point out that it's not valid as you have never seen it and it's not signed by you.
Also, its wrong of a previous reply to state that the check out is your choice of time. I'm afraid you'll usually have to fit in with the Inventory Clerk or Agent's time.