I'm wondering how much protection NHL referees wear aside the helmet. I've seen referees that had to either leave game or where on ice for a long time after getting hit or falling awkwardly. Those incidences have made me believe that the referees wear considerably less padding than the players.
Referees and linesman are not obligated to wear any padding besides their helmet . However, as you have noticed, often times officials either get hit by players, the puck, or they fall and hit the ice hard.
Almost all (if not all) officials therefore do wear padding under their uniform. Per the National Hockey League Official's Association website:
They are protected by pads that cover the shins, calf muscles, knees, hips, thighs, hamstrings, elbows, lower back, and kidneys. Some officials also wear flak jackets to protect the rib cage and torso.
NHL officials can decide what type of equipment best suits their need and they can pick and choose what they like from a vast array of options. The equipment that National Hockey League officials wear mimics the padding that the players wear but is generally lighter, more flexible, and more compact. The skates and headgear that NHL officials wear is, in most cases, exactly what the players are wearing in The National Hockey League. 
The reason they wear smaller padding than the players is because they are not regularly getting body checked, nor do they regularly block shots. Players also get hacked at by sticks on a regular basis, where the officials do not. In addition, the officials need to be able to keep up with the players all game and are generally not quite as fit, so the lighter padding helps.
 http://www.nhl.com/nhl/en/v3/ext/rules/2014-2015-rulebook.pdf, rules 31.1 and 32.1.