Can clients reply to the emails sent by the system?

Yes, clients can reply to the messages sent to them in most cases. The 'reply to' address depends on a few factors, such as whether the email is sent manually or automatically and if you have an Email listed under Setup > Company. More on the specifics below:

Automatic Emails (e.g. reminders, followups)

When you have an email listed under Setup > Company, the 'reply to' address for automatic emails is set as this email address.

When you don't have an email listed under Setup > Company, clients wouldn't have the ability to 'reply to the email.

If you'd like clients to reply to automatic messages, add an email under Setup > Company.

Manual Emails (e.g., confirmations on appointments booked internally)

When you have an email listed under Setup > Company, the 'reply to' address for manual emails is set as this email address.

When you don't have an email listed under Setup > Company, the 'reply to' address for manual emails is set as your user email. (i.e., the email address you use to log in, which you can update under Account > My Profile)

For more on how the emails appear to your clients, please refer here.