Hello Huang,
I think both strategies would work well for data import. Keep in mind that dada2 requires the unjoined data (it uses it during quality control), so if you wanted to use dada2 you have to ask for the unjoined data. If you want to use deblur or vsearch for denoising or clustering, you could import the joined data directly.
I think both strategies would work well and would be highly defensible.
Your second question is very common:
Yeah, why isn't import listed as a plug-in?
According to the developers, the tools import command is a 'built-in' command that's included with Qiime 2. So because it's included with Qiime 2, it's not technically a plug-in. Isn't that confusing?
But plug-in or built-in, you can run
qiime tools import --show-importable-types and --show-importable-formats
to see all the types and formats currently supported.
Let me know if that helps answer your question!
Colin
Happy New Year! 