Opening of encrypted sparse bundle in El Capitan very slow

I have a 76GB encrypted sparse bundle on the rMBP SSD drive. Mounting it by double clicking it in Finder was pretty much immediate in Yosemite.

With El Capitan a popup appears with "Verifying 'name of sparse bundle'" and a progress bar. The progress bar shows no progress and after fifteen minutes or so the popup disappears and the password entry dialog box appears. After the password has been entered the sparse bundle is finally mounted.

When I run the Disk Utility First Aid function on the mounted volume it finishes in a few seconds and reports no errors. Console does not seem to show any related messages during the mounting.

Is there any reason why this popup appears and is there a way to circumvent it? Fifteen minutes to mount a volume is just not practical.

I also had a sparse bundle that was very slow (>1 minute) to mount, but I solved this (it now mounts in seconds) by turning off automatic file system checking. Before I figured it out, this would happen:

hdiutil attach -verbose ~/the.sparsebundle paused at this line:
Checking volumes…
and it would appear in Activity Monitor as hdiutil using 100% CPU, for over a minute at a time, depending on connection speed.

To speed things up, pass the noautofsck option to hdiutil, like so:
hdiutil -noautofsck ~/the.sparsebundle

Or if you are mounting any other way, set the system preference:
defaults write com.apple.frameworks.diskimages auto-fsck -bool NO

It is possible your update to Sierra resulted in a default being reset and/or a bugfix, per the hdiutil man page:

By default, only quarantined images (e.g. downloaded from the Internet) that have not previously passed fsck are checked.

You could turn off the automatic file system checking and then check the output of diskutil verifyVolume /Volumes/theSparseBundleVolume occasionally, as a balance between data integrity and convenience. Keep in mind, that diskutil command will unmount your volume.