1. If the datastore is 600GB and shows 100GB free in vSphere, is the full 600GB shown as allocated on the SAN?
It depends, if for example in certain time you utilized 550GB on datastore and deleted 50GB, maybe there will be 550GB allocated on the SAN, since space reclamation is not done automatically.
2. We are running vSphere 5.1. If I run "vmkfstools -y 50" to reclaim 50% of free space, what happens to the SAN?Using the example of 100GB free space on datastore, if you use vmkfstools -y 50, the command will create a balloon file that is 50% of 100GB in size (50GB) and after file is created, it will be removed zeroing the space and free up the space on the SAN.
3. Does the reclamation only affect deleted blocks, or does it affect all free space?Not 100% sure, but I think it depends of how many space do you want reclaim, if there is for example 100GB free on datastore and 50GB free on the SAN and you use vmkfstools -y 70, the balloon file will fill up not only the 50% of deleted blocks but more 20% of already zeroed blocks... but of course after the command completion, you will get the 70% of free space :-)