Well that’s a difficult one, and you are in the best position to answer this for yourself since you know the individuals involved, and are most likely to know how they will respond.
Even if there is no specific policy, your employment contract may stipulate what you can or can’t do regarding references and contacting clients once you have left.
The owner of the company is the best person to provide a reference. Even if he doesn’t like you leaving he should provide an honest opinion of your abilities and qualities, also many recruiters will not accept a new employee unless they have a reference from your most recent employer (for example the NHS will not hire an employee unless they have a reference from their current or most recent employer).
That said, your question seems to be more a question of whether it is ethical to ask clients for a reference, and this has to be down to your own morals.
If you are not planning to leave immediately it might be worth creating a LinkedIn profile, and asking clients, colleagues and your boss to provide endorsements or recommendations for you and the company. This may avoid you having to specifically ask in a letter, and can be seen by future employers.
If you do decide to send an email to clients, it would be best practice to ask the owner of the company first. The wording of your proposed email seems reasonable. It would probably be best to send this from your company account, but I understand your concerns that you may not have access to the account, in which case you could send it from your personal account.
I hope that has been of some help, and good luck!