Deleting srt files from vlc app in iPad Mini
So you have lot of subtitles hanging around loosely. There are two ways you can remove these annoying creatures. I will discuss both of them, use whichever suits you best. 


Delete and re-install the VLC app.
Take a deep breath, this is going to be long. There is a work-around that I've found and works 9/10 times. 


Theory: 

What VLC does in the background is that, it deletes the subtitles files automatically  whenever you delete the parent video file, provided that the video and the subtitle have same name.

For example, if your video file is named "test.mkv" then the subtitle file should be "test.srt"

What you need: 


A video clip, format doesn't matter, and smaller the size is
better as it will take less time to get copied.
iTunes


Procedure:


Connect your iPad to your computer and go to iTunes.
In iTunes, go the "Apps" section of your iPad and find your way to VLC.
Copy all the parent-less subtitles to one folder in your desktop.
Create copies of the video clip as many as the number of subtitles present in that folder. For example, If you have 4 subtitles, then you create 4 copies of the same video clip.
Rename each video clip to one of the subtitle. Take caution while renaming, don't change the extension/format of the video clip.
Once you have the video clips renamed, copy the video clips to back to VLC. 
Save and eject the iPad from iTunes and computer. 
Go the VLC app in your iPad and start deleting those renamed video clips.


So, as per the theory, when you delete the video clip, VLC will delete its subtitle as well simultaneously.