We are currently shipping several scripts in xstartup.d. If a customer disables one of these, say tl-clipboard-helper, and then upgrade ThinLinc, the disabled script will return. This is perhaps not what the customer wants. The same type of problem exists with Linux .d directories in general, say /etc/cron.d, /etc/yum.repos.d etc. Most tools called from xstartup.d can be disabled by some other means such as via Hiveconf configuration files; I believe tl-clipboard-helper is the only exception. In any case, we should perhaps consider creating some functionality for permanently disable shipped xstartup.d scripts. See also discussion in komintern, starting with article 303696.
A similar problem is that we recommend removing the setuid bit from tl-mount-personal as a good way to disable local drives. But like xstartup.d scripts, that bit will get restored on upgrade.
