Japan's aircraft excelled at speed, manueverability and flight range, but this cost them dearly in the long run because their pilots suffered terrible attrition. My question is are there any exceptions to this? Did Japan use any planes with armor or upgraded structural durability? Did they have any prototypes like this? If so, did said planes see any service?
I think we'll have to clarify here.
I'll assume that due to the mention of high attrition rate, long range, and maneuverability you're referring primarily to the A6M series of planes. Or colloquially known as the Zero.
The Zero was indeed a very advanced plane during it's inception in 1939. With the first Zero the A6M2. Offering a very very long range, relatively forgiving landing characteristics and an incredibly lightweight body that excluded safety features such as self sealing fuel tanks and armor plating the initial version: the A6M2 became a very light, and maneuverable plane thanks to the high lift and low wing loading on a very light chassis.
In comparison the 1939 and 1940 iterations of the Zero would face relatively light competition. The less maneuverable but much more heavily armored F4F Wildcat in the pacific and the less maneuverable P-40, although that was taken care of by the also light and agile Ki-43.
In terms of speed, Japanese fighter aircraft weren't much faster than their American counterparts. Although the A6M could out maneuver the F4F, but the time the much more powerful and faster F6F and F4Us were introduced, the A6M quickly saw it's advantages removed. Any lack of maneuverability in the horizontal axis were neutralized by the sheer differences in speed. By 1942 the Zero was beginning to see the zenith of it's ability. Successive modifications and upgrades in the form of the clipped wing A6M3 mod 32 with the 1150HP supercharged Sakae-21 and then the shorter winged (some say prototype A6M5) A6M3 Type 0 Mod 22 that corrected the reduced lift of the mod 32 all would prove ineffective at catching up to the rather effective tactics of the durable F4Fs and later the speed of the F6F.
That's not to say that the A6M was a bad plane in question. It's attrition rates were due to experienced flight pilots in the IJA and IJN being in constant rotation as opposed to being brought into the rear lines to provide training. As such pilot quality decreased as more experienced pilots began to suffer more casualties. Coupled with the lack of an armored variant with self sealing tanks until the much later A6M5s and A6M6s and we see that the Zeroes became much less effective given the lack of speed and poor development progress on the Water-Methanol Injected Sakae-31 (which was rather ineffectual during it's introduction due to the unreliable injection and the extra weight on the already overburdened platform.
So in regards to the A6M series, it wasn't that upgrades weren't done. Multiple versions of the Zero progressively increased armor, added self sealing tanks, uprated armnament, redesigned wings, addressed control stiffening and increased power in the engine. The problem was that all of these features added a significant amount of weight and the Sakae engine platform was beginning to show it's weakness by 1943. Coupled with the a much faster opposition in the form of the F4U-1d, the F6F-3 (and later the much faster F6F-5) and the P-38s, it's no surprise the A6M Zeroes had such a large attrition rate.
There were however, successors to the A6M that proved to be much safer. The J2M Raiden was capable of matching US aircraft with it's much more powerful Mitsubishi Kasei engine. Although it was designed to be an interceptor craft, it was much less fragile compared to the already outdated A6M series.
Likewise, the IJA developed the Ki-61. The spiritual successor to the rather successful and lightweight Ki-43 employed armor plating and self sealing fuel tanks. Unlike most of the other later Japanese planes, the Ki-61 did not suffer from as many teething issues as seen on the Kasei engines or the Nakajima Homare.
The Ki-61 however soon also became obselete. Despite it's high wing loading and medium altitude interceptor role. The DB-601 derivative the Ha-40 soon proved to be inadequate in providing enough speed for the Ki-61. Nevertheless, aside from the A6M Zero, Japanese aircraft tended to have decent protection for the pilot. And many other planes like the N1K and the Ki-84 also saw service. However these planes were not produced in significant numbers to cause a large impact in the war.
After all this digression I suppose the short version would be: Yes, there were Japanese fighter aircraft that were more structurally intact and more armored than the A6M series. But aside from the Ki-61, planes like the N1K, the Ki-84, and the J2M weren't produced in significant quantities to make a large impact. Furthermore, regardless of armor, Japanese air doctrine and employment of the the A6M series against much faster planes would cause a surge in attrition rates all the same.
Sources: