Hi, sorry to hear you are having this problem. I have not run into it myself. I created an EXFAT partition on an SSD (I did it on the Mac, fwiw). Then, I put some images into the root of the volume and inside a folder in the volume. I added both to Nitro. Then I selected images in each of the root and the folder and then used the trash icon to delete them. Both worked fine and the app continued to run without freezing.
Can you find a crash log or something that I can look at? You can find those in Settings > Privacy > Analytics > Analytics Data and search for the app.
Also, do you have problems deleting files if they reside in a folder on your iPad, rather than the external disk?