Gordon Stanger covers the climate aspects well in his answer, but I thought I'd chime in with an answer to the "was it as much a desert as it is now?"
While I'm not aware of any archaeological evidence for the agriculture in the land surrounding Masada at the time of the siege, there are several factors that may have, at that time, made the area less 'deserty.'
There are two in particular I want to mention. The first are qanats. This technology spread from Persia around ~500 BC and quite impressive ones were built by the Romans in dry places, like this one from modern day Jordan.
Masada is in a cliff overlooking the Dead Sea, but the top of the fortress is only about 60 meters above sea level; the surrounding land is much lower. This puts it in a good position to receive water from nearby groundwater at higher elevation. As can be seen in Google Maps, The land rises 200m in 2.5 km to the West, and 400m in about 5.5 km. Google Maps even indicate the course of several wadis that flow in the general direction of Masada which could be used as the basis orfor a partially underground irrigation system.
Qanats take a lot of work to build and maintain, but in a land where there is cheap labor and little water, it can be worth it to build them. The Middle East at the time had plenty of desert adapted trees that could thrive with a little irrigation (almonds, olive, carob, date, pistachio; all mentioned in the Bible), so it is entirely possible that there were groves of desert trees in the land around Masada.
This brings us to the second point: tree cover. The tree cover currently existing in the area around Masada (i.e. none) doesn't have to be the tree cover that was always there. Trees being rare in the southern Levant, they were always under pressure for use as firewood, and their regrowth was always limited by grazing, especially by goats.
There are several trees (large shrubs really) that can grow in such hot and dry conditions, as they are present in the rest of the Negev desert in Israel, such as Acacia, Pistachia, and Tamarix. Acacia in particular may be a keystone species, such that higher, ancient levels of tree cover could have encouraged a generally greener landscape.
In conclusion, while the area around Masada is drybarren now, it does not have to have been 2000 years ago. There were labor intensive irrigation techniques and tree crops available to make successful farming a possibility, and a lower firewood and grazing pressure from a lower population may have allowed the wilderness areas to have been greener than they are today.