Sofia,
Do you mean tokens in the email? Or tokens in a program which uses MSI as the way to send the emails etc? Or tokens in the email for "Send Marketo Email"? Can you be more specific?
Since the emails are "housed" in Marketo and referred to in the emails, if they are on the template they will definitely work. I have used them numerous times as signature lines for my reps, From/Reply to email fields etc.