As anyone reading this post is unlikely to know your exact configuration and past history re your installations/uninstallations, the best way you can proceed is to experiment yourself. Before you do anything i would suggest that if you have some files within your installation but they are not causing you a direct problem then leave them. They should only worry you if you are seeing a particular problem(s) with a module or are trying to reinstallation/upgrade of a module(s). Otherwise old files will only be taking up disk space and most hosting environments give ample room.

I have not fully checked what occurs during a module installation, but i would expect that

- Records are added/updated to some of the dotnetnuke system tables within the database, 
- Depending whether the module is a new installation or reinstalltion/upgrade. Modules will overwrite previous files with later ones and delete/recreate database tables/records as required. I.e. previous installation files will not neccessarily be deleted and will hang about with the dnn installation doing no harm

Upon uninstallation (using the module control area with host menu)
- Dotnetnuke' system' records will be removed by the dnn core. 
- Tables/records created in the database and files within the web site created with the module itself (e.g. tables starting with 'store' for the store module), then the tidy up will vary between modules. Depending upon whether the designer felt it was neccesary or indeed could be bothered to put the extra effort in to write the sql deletion/removal routines. 

Opening the .dnn manifest file within a modules installation zip file will give you a pointer to the areas within the site that will be affected/used. 

I would suggest not to delete any suspect files on your main production environment without first experimenting in a 'Test' environment. I  would also not delete them but simply move them out from the dotnetnuke installation into an alternative location, logging down where they were moved from in case you find a problem and have to move them back (gradually or all at once)

You can create your test system as follows...

- Ensure you have a complete backup of both the web site and database (taken at the same time i.e. snapshot of your complete DNN installation. I use DbGhost, i believe there is a DNN backup module on snowcovered. 

- Install the snapshot backup on a local instalation (i.e. your laptop and run it as localhost) or within your hosting package if you can have another mssql database (you may need your hosters help here to rename your database copy), and remember to point to the new database name within your webconfig file and use a different domain.

I don't think that clearing out old files will help the performance of your dnn installation. The only areas that can significantly affect your sites performance are

- Badly written code
- Extremely large database with lots of records and poor indexing, normalisation
- Slow/low specification hardware or shared hosting hardware overwelmed at busy periods

There are other areas, e.g. caching etc, but the above are the starting point for locating basic improvements...

The primary focus for Version 4.4+ was performance and speed, therefore if you are seeing poor permance on any areas of your site then inspect which modules are being used on the page(s), hone in on which one could be causing the problem, as each module on a page is probably wriiten by different developer(s) with varing levels of skills...

One last point if you have been adding and deleting large amounst of modules and pages then empty the dotnetnuke recycling bin, probably won't make huge performance  differences but will reduce the records with the dnn system tables and files. Note: You probably won't recover any database disk space from these kinds of deletions as most databases require the administrator (hoster) to run some kind of compaction routine to reorganise the physical tables/records areas.

Sorry i can't be more specific to your question

Regards
Bryn
http://www.planetspringwell.com