In many strategy games that I've either played or watched, specifically age of empires 2 and atilla : total war, camels get a bonus attack to other cavalry. Are camels normally considered to be natural counters to horses?
There are potentially three questions here:
I'll attempt to answer the third. (For the first and second, while you wait for other answers you might want to check out these former AskHistorians questions: 1 2 )
While strategy games have been around for over a thousand years (depending on how you define it), the earliest examples that are analogous to computer strategy games like Age of Empires and Total War (in that you have discrete units with extensive special rules based on their class) are miniatures/board games from the second half of the 20th Century.
These games tried to model or simulate historic battles, or abstract or novel battles with historic armies. A number of ancient sources described camels spooking horses because of their smell and appearance, including Herodotus, Xenophon and Procopius. Particularly interesting is Herodotus, because he describes the use of an army's camels to spook the enemy's horses, without those camels spooking their own army's horses.
When Cyrus beheld the Lydians arranging themselves in order of battle on this plain, fearful of the strength of their cavalry, he adopted a device which Harpagus, one of the Medes, suggested to him. He collected together all the camels that had come in the train of his army to carry the provisions and the baggage, and taking off their loads, he mounted riders upon them accoutred as horsemen. These he commanded to advance in front of his other troops against the Lydian horse; behind them were to follow the foot soldiers, and last of all the cavalry. ... The reason why Cyrus opposed his camels to the enemy's horse was because the horse has a natural dread of the camel, and cannot abide either the sight or the smell of that animal. By this stratagem he hoped to make Croesus's horse useless to him, the horse being what he chiefly depended on for victory. The two armies then joined battle, and immediately the Lydian war-horses, seeing and smelling the camels, turned round and galloped off (source)
One of the earliest of these miniatures games is the game now called Ancients 1st edition, which was released in 1969. Already, we can see on page 14 that cavalry suffer "disorganisation and distraction" when near camels (or elephants) (and the game even accounts for whether the cavalry would be familiar with the smell of camels).
Ancients was influential in the wargaming community over several decades and seven editions, and its spiritual successor De Bellis Antiquitas (DBA) (1990) which was popular (relatively) in its own right describes camelry as "camel-mounted warriors" whose "chief value was to disorder a superior enemy's horses" (p 3). However, I can't see that this was reflected in the rules (see e.g. p 9).
The 1976 game Classic Warfare, by Gary Gygax (co-creator of Dungeons & Dragons) also had rules for camels, although I can't find a copy to see if they had a special effect on horses. In any case, I think a combination of the historical record and the influence of Ancients/DBA explains why this is such a common concept in strategic tabletop games.
There were also more recent examples of horses responding badly to camels, including a US Camel Corp "experiment" in the 19th Century. The US Army Museum mentions in passing that the scent of camels spooked horses that were unfamiliar with it (source). /u/Zither13 talks more about that on this AskHistorians thread. However, the fact that these special rules about camels seemingly appear in ancient wargames, not medieval or modern ones, suggests to me that it's the ancient historians who introduced the concept to wargaming.
I don't know of any RTS games that had camels in them that are older than 20 years old (Age of Empires II is the first I know of). While there are some genres of computer games that were heavily influenced by tabletop games (roguelikes being the most obvious example), that doesn't seem to be the case for RTSes - so these designers may have been directly inspired by the original ancient sources, rather than through the tabletop wargames.