The Credant software can be uninstalled by administrators, but not generally by end users short of the previous wipe/reinstall suggestion. Note well that the software has an audit system that allows administrators to be aware if the software does not check in within their configured monitoring period. So if you did uninstall, you can expect them to be aware that you've done so.
If performance is a concern, you could reach out to your administrator to ask whether they can tune your policy for a development environment rather than the typical business user's arrangement if they haven't already done so. If you need to track down the administrator to contact, you could email the support group at Credant and ask them to point you in the right direction.
In my experience, worrying about outer track versus inner track is no longer worth the effort. The difference in performance is just too small, when factored against other performance impacting things (RAID, caching, filesystem fragmentation, etc).
However, to answer your question directly, there is definitely still a reason to keep a decent amount of free space on a modern hard disk (especially rotational (non-SSD) disks), and that's file fragmentation and seek time. When there is a good amount of free space, files can be written sequentially, allowing them to be read in without multiple seeks. This allows a file to be retrieved much faster than if a disk head has to seek all over to pick up little chunks of a file.
This article/blog post is more targeted to file fragmentation than disk performance, but it offers one of the better explanations I've found for file fragmentation and why available free space impacts it: Why doesn't Linux need defragmenting?
The more a disk fills up, the more files (especially large files) will become fragmented and slower to read and access. This is also the reason that Linux filesystems reserve a percentage of space (usually 5%) that is only available to root. This reserved space is very useful for emergencies (so a user can't completely fill a disk and cause problems), but primarily intended to reduce disk fragmentation as the disk fills up. When dealing with very large files, as are common with databases, the fragmentation problem can be reduced by pre-allocating your data files (assuming the database (or other application) supports it).
In these days of very large and relatively inexpensive disks, there is rarely a valid justification for letting a filesystem reach capacity. This is even more true in situations where performance matters.
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The "HP Protect Tools" is a rebadged McAfee/Safeboot FDE product. The performance impact shouldn't be too bad -- I'm assuming that you're using AES.
We encrypted about 5,000 laptops three years ago, and our folks didn't report any significant performance issues. A few older boxes blue-screened, that's about it. You may be experiencing slowdowns immediately after enabling encryption... encrypting the disk can take 8-20 hours depending on the vintage of the equipment and size of the disk.