Your questions are too vague to be answered very concretely. However:
- The packages are almost identical but there are some small differences.
- Yes you can do encryption.
- It is impossible to say whether or not ARM is more secure or not than x86.
ARM does not manufacture any chips but only allows numerous manufactures to use the design to make ARM-based systems. As a result the amount of different ARM-based chips out there is massive. Not only that, but there are many different versions of ARM. (hardfloat supporting/not/32bit/64bit/there families Coretex A, R and M and so on). They are often combined with other processors. Because of this, it is not possible to make a general level claim that one or the other architecture is more "secure" than the other. Besides, the vast majority of security issues do not relate to what processor architecture is running the software but rather stem from problems relating to how the software was designed or configured.
When you want to know whether or not a package is supported for the device on Debian, look at the packages web database. For example:
https://packages.debian.org/jessie/ecryptfs-utils
Scroll down to the bottom of the page and click on the architecture you are using. I'm guess that machine would use arm64 and possibly be "backward compatible" with armhf. There you can see if the package exists in that arch and what version it is.
If you ever encouter a package that does not exist, you can still compile for it on a x86 machine using a cross-compiler
You can also install Debian arm64 on a virtual machine to check it out before making a decision. I have run Debian armf on qemu and it worked ok.