Apologies for the necro, but as I came here from google experiencing something similar and found some good information but no real conclusions (seems OP ended up just avoiding using ._ files) here, I thought I would record my findings dealing with this behavior.
My conclusions:
With 'Hide "dot" files' off but 'Enhanced macOS interoperability' on, any existing files on my array whose names began with "._" would not appear over SMB, and an SMB client with write permissions was not able to create them. (Files just beginning with "." work fine)
Disabling 'Enhanced macOS interoperability' did fix this; "._" files are both visible and can be created over SMB after setting it to 'no'
'Enhanced macOS interoperability' was on by default, at least on my (two) installations of version 6.12.8. Hide "dot" files was off by default.