UPM does a REST call to enable/disable plugins. Calls are done to <jira url>/rest/plugins/1.0/<plugin key>. The content contains info about all the modules. Please try doing a sample enable/disable using browser and check the details of the PUT request being done.
As a general rule, configuration files are read as something starts up. For the system side of it, this means you restart Jira if you need to amend config files. If you're looking at plugins, it's catch-22 - you need to re-read a changed config file, and in order to do that, you need to, um, restart the plugin.
There are no methods exposed via REST, SOAP etc that I know of, or can find at a glance.
So, I suspect your options are:
Sorry, not enough coffee this morning.
Most, if not all, of the plugin enabled/disabled state is controlled by entries in the database. You could change these using SQL, but
1. Some plugins need to know they are being enabled/disabled - Greenhopper for example. Changing their state in the database can break them
2. You MUST have Jira down while you change data using SQL, even for a minor change like this. If Jira is running, then your change may well be completely ignored, or, more frighteningly, trash your setup.
By breaking, I mean data loss and having to remove them and put them back, re-indexing, and having to repair bits of your database. I really can't recommend using the UI to do this instead of trashing your data.
I'm curious though - what makes you want to do this? Enabling and disabling plugins in the UI is quick and I can't think of a good use-case for doing it by hacking. It's not worth the effort as far as I can work out.
as answered a minute ago in How to Enable Disabled Plugins in JIRA:
the pluginstate is saved in the database and has it's own table, called ...
Example for an postgreSQL DB:
jiradb=# UPDATE pluginstate SET pluginenabled=
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