Matrix supports end-to-end encryption between users in encrypted rooms. Not all rooms are encrypted, and most bots and bridges do not support encryption out of the gate. With the bot-sdk, encryption (or crypto) needs to be turned on deliberately in the code.
The following guides go into detail on how to enable encryption for different use cases:
General principles
For both bots and appservices, an ICryptoStorageProvider will be needed to actually enable encryption. Eventually this will be able to be your own implementation, but for now must be a RustSdkCryptoStorageProvider or derivative.