Is whipple's disease usually deadly?

No, but must dx & rx: Whipples disease is a very rare condition, often found in middle age men, that is also called lipodystrophy. It a bacterial-caused disease that leads to malabsorption of mostly fats and certain sugars into the bloodstream. It will lead to nutritional deficiencies among other problems. Need rx with antibiotics, usually at least a year, herbs and supplements. If left untreated, it can be fatal.

Untreated, yes: Historically, untreated whipple's disease was 100% fatal within a few years. Thankfully, it's quite easy to manage though you'll be taking antibiotics for a long time.