Can one feel mostly happy and anxious-free but still experience suicdal thoughts? On endep (amitriptyline) 10 for 6 months.

Yes. And make sure you discuss directly with a primary care doctor, a psychotherapist, or psychiatrist asap, especialy in relation to the medications you take. Do this immediately. The medicines can make you feel ok because that's how they work, by increasing the "happy" neurotransmitters in your body. But if the underlying issue is not dealt with , you can still have suicidal ideations.