No - new zones added dynamically don't go into named.conf or any include
files of named.conf (these I suspect are part of a default OS
distribution default set-up that you've adopted, but include files are
often used anyway).
They go into another file or database that named accesses at start-up
and maintains thereafter.
See BIND 9.18 Administrator Reference Manual:
allow-new-zones
Grammar: allow-new-zones <boolean>;
Blocks: options, view
Tags: server, zone
Controls the ability to add zones at runtime via rndc addzone.
If yes, then zones can be added at runtime via rndc addzone. The default
is no.
Newly added zones’ configuration parameters are stored so that they can
persist after the server is restarted. The configuration information is
saved in a file called viewname.nzf (or, if named is compiled with
liblmdb, in an LMDB database file called viewname.nzd). “viewname” is
the name of the view, unless the view name contains characters that are
incompatible with use as a file name, in which case a cryptographic hash
of the view name is used instead.
Configurations for zones added at runtime are stored either in a
new-zone file (NZF) or a new-zone database (NZD), depending on whether
named was linked with liblmdb at compile time. See rndc - name server
control utility for further details about rndc addzone.
https://bind9.readthedocs.io/en/v9.18.31/ or
https://downloads.isc.org/isc/bind9/cur/9.18/doc/arm/Bv9ARM.pdf
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