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It depends on your directory and database layout, and what you tell Akeeba Backup to do.

Let's say that you have the following disk layout:

<home folder>
  |
  +-- public_html
  |      |
  |      +-- sub1

Where public_html is the web root of your site and sub1 is your subdomain root. In this case, the subdomain web root is a subdirectory of your main site's web root and its contents will be backed up by default (unless you tell Akeeba Backup otherwise).

However, if your disk layout looks like this

<home folder>
  |
  +-- public_html
  |      
  +-- sub1

then the subdomain root will NOT be backed up by default as it is NOT a subdirectory of your main site. If you want, you can tell Akeeba Backup Professional (not Core) to back up that directory as an add-on directory, or tell Akeeba Backup Professional (not Core) to use sub1 as the root of the site to back up — Akeeba Backup Professional has a lot of options to help you back up additional or alternative sites.

It is similar for the database.

If both sites share the same database but with a different database table name prefix (e.g. m41n_ for your main site and 5ub1_ for your subdomain) then, by default, all tables will be backed up i.e. the tables of both the main site and the subdomain unless you explicitly tell Akeeba Backup not to do that through Database Tables Exclusion (Core and Pro versions) or RegEx Database Tables Exclusion (Pro version only).

If the two sites are using different databases (different database names, not just database table name prefixes) then only the main site's database will be backed up. Unless, of course, you tell Akeeba Backup Professional to either include the subdomain's database as an add-on database, or use it as the database of the site to back up — Akeeba Backup Professional has a lot of options to help you back up additional or alternative databases.

So, no matter what your disk and database situation is, you can tell Akeeba Backup Professional to do what you want it to do, and it will do it. It is very flexible.