I feel quite comfortable classifying encrypted messaging apps in the same category as houses and chain mail, even if the US government has historically disagreed.
Only if that logic is sane, which it isn't.
There is an difference between doing something directly and indirectly. Anything can do anything given enough indirection. There is no plausible way in which your ordinary use of encryption or body armor could directly harm anybody else. There are some immediately obvious ways that your ordinary use of a howitzer could directly harm somebody else.
And the right to defend yourself using indirect offensive measures has no inherent symmetry with the right of government (or lack thereof) to prevent you from defending yourself using direct defensive measures.
And the same attack works if instead of encrypting your data they upload a copy of it to their servers before deleting it. Albeit less efficiently, so we're back to indirect harms.
You have listed three things which are all really the same thing. There is no objection to private ownership of motor vehicles or ships. You object to the weaponry.
But we can put aside the whole right to bear arms debate in this case because there is an obvious way to distinguish it. Encryption is a purely defensive technology.
It is totally illegitimate for a government to prohibit things like armor and electromagnetic shielding, even if some of them do, because these things only defend, they do not attack.