From a HDD protection stand point, is it better to leave my desktop always on for the whole day, or is it better to let it Suspend/Standby after a given period of time (say 30 minute)?
That depends on your usage.
The most harm is done to a drive by spinning up after suspend/standby. The less you do that the better. But leaving it running also slowly wears parts.
If you are going into standby every 5 minutes only to wake it up a few minutes later: leave it on.
If you have to choose between standby during the weekend or leaving it on it is probably best to go to standby.
I know that these are two extremes. But we have no idea what your average usage is.