In manga up to chapter 1086, the only people that have been stated to be aware, prior to the discovery of Gear 5th, of the true nature of Gomu Gomu no Mi are the Five Elders and, implicitly, Imu. After the awakening of the Devil Fruit, Kaido seems to have figured out that Gear 5th is a zoan ability and Vegapunk seems to have made 2+2 with Gear 5th looking like Nika and Gomu Gomu no Mi not being on old records.
In chapter 1 Shanks and his crew refer to the fruit as Gum Gum, and more generally the entire One Piece manga is completely consistent with Gum Gum being the fruit of rubber up until Who's Who starts telling his backstory to Jinbe in chapter 1017 (personally I would say until the actual awakening and explanation in chapters 1043-1044, but let's say that the first hint was there). So the reasonable guess should be that Shank's crew did not know, all the more because they did not keep it for themselves.
The only argument towards Shanks having knowledge of the Gum Gum fruit being important (which doesn't necessarily imply that he knew that it's a mythical zoan, or that it was somewhat related to a world-shaping force) could come from Shanks' flashback in chapter 1054, where he recalls the assault to the WG ship that was carrying the fruit. In that flashback, young Who's Who is surprised that a pirate would go to all that trouble to assault a ship that was carrying a rather unremarkable devil fruit. However, in that memory Shanks just says that he does not care if the ship is guarded by a CP9 agent. He does not say anything remotely close to "It is paramount that we seize that special fruit". It's still consistent with them just being in a regular raid for plunder. Even Who's Who claim that the DF shouldn't be worth the trouble is somewhat inconsistent with Devil's Fruit being per se rare and precious items: for comparison, it is claimed in chapter 19 that Buggy's Bara Bara no Mi could be sold for 100 million Belly.
As for your claim that Shanks has been protective of Luffy's fruit rather than Luffy as a person... Well anything can be retconned, and Shanks will be be expanded upon in the last arc. However, so far Shanks has been depicted as protective towards Luffy because of personal affinity and because he has always seen potential in him. More generally Shanks has always been friendly towards anybody who had "good alignment". The most notable example would be Whitebeard and his crew, when:
- he foresees that Ace fighting Blackbeard may lead to the death of Ace and Whitebeard, and he meets with the latter to warn him;
- he steps in to end the battle of Marineford and save Whitebeard's crew and Luffy.
Also he [Shanks] lost his Arm just to motivate the luffy to be worthy of use this legendary fruit.
It seems far-fetched: it's quite clear from chapter 1 that Shanks lost his arm to save Luffy's life, after he was put in mortal danger by a sequence of unexpected events.