Deleting unused Distribution modules
By disabling modules enabled by the profile, you may be working against yourself.  There is known issue that D7 does not enforce module dependencies listed in the .info of a profile.  So if some of the modules you are disabling were enabled on install because they are listed in http://cgit.drupalcode.org/commerce_kickstart/tree/commerce_kickstart.info, then you will find that the profile itself is actually disabled.  You can tell if this has happen by looking in the system table and/or the status report.  In the system table, the status on of the profile will be 0.  In the status report you'll see the profile's name, but no version number. You can read more about the D7 issue in https://www.drupal.org/node/1170362.  Some progress has been made on addressing this in D8 in https://www.drupal.org/node/820054.  

Because Drupal also uses a variable to tell which profile is being used, a disabled profile may not cause any issues beyond preventing update status lookups.  But if a module is being included as a dependency in the .info, it's worth taking the time to understand why the profile's maintainer added that dependency in the first place.  

As far as removing modules with a status of 0 to achieve a slightly smaller system table, that is unlikely to have a measurable impact on performance.  Where you may see a performance hit is from lots of extra .info and .install files. Creating the list of modules at admin/modules requires scanning several directories for .info files.  Checking for updates scans the .install files for any update hooks that haven't already been applied.  Beyond that, modules that are not enabled shouldn't be impacting the performance when Drupal renders a page.

You should consider using https://www.drupal.org/project/profiler_builder to generate your own profile and .make from one of the sites you built from scratch.  That would give you the advantage of getting another site started quickly without the overhead of a general purpose kickstarter style profile and distribution.

If you do create your own profile, please consider sharing it on Drupal.org so that other members of the community can benefit from the a more efficient (while less robust) Commerce configuration.