Learn Italian: Il paziente aspetta in ambulatorio. - The patient waits in the doctor's office.

Nouns ending in -e can be masculine or feminine. To specify a female patient, you just change the article to feminine: la paziente. Here, il paziente tells us the patient is male or is being referred to in a general sense.

Since this lesson covers commands, could aspetta be an imperative here?

Not in this exact sentence, because il paziente is the subject performing the action ('The patient waits'). However, aspetta is identical to the informal command 'Wait!'. If you dropped the subject and just said Aspetta in ambulatorio!, it would be a command meaning 'Wait in the clinic!'.

Why is it in ambulatorio instead of nell'ambulatorio?

Many specific locations in Italian take the simple preposition in without a definite article when you are there for its typical purpose. Just like in ospedale (in the hospital) or in banca (at the bank), you simply use in ambulatorio.

Is ambulatorio the only word for a doctor's office?

No. Ambulatorio often refers to a clinic, dispensary, or an outpatient ward in a larger facility. If you are going to a doctor's private practice, you will often hear it called lo studio medico or simply lo studio.