I think it would depend on who did the developing of said art. For example, classical Japanese MA, what’s now called Koryu, was developed by soldiers and warriors and thus weapons usage was placed first on the list of things to master. Empty-hand skills the form of jujutsu (sp?) developed as an adjunct to weapons skills. This is obvious when you consider that on the battlefield, the guy with a sword, spear, stc was far more advantageous than one without weapons. When there was a lull in the cycle on warfare and peace, you had the soldiers taking their battlefield skills and experimenting with them, trying to find use of them in non-battlefield conditions, i.e. out about town, in the castle, in the alleyways, etc. That’s why a lot of jujutsu styles nowadays have a basis in swordsmanship and kenjutsu movements.
In China, I’d say the same thing happened, except over an even longer period of time. For although Japan had a nominal Emperor, civil war didn’t really stop until the Tokugawa Shogunate. In China, once an Imperial Dynsty was established, there were relative periods of peace when the country was not wracked by constant warfare. Taking Shaolin as an example, the fist methods of Shaolin didn’t develop in a vacuum. Many veterans of fighting who did not want to deal with the chaos often entered monataries. The idological framework of using physical exercise as another method of obtaining enlightenment (notice I say physical exercise not necessarily fighting skills as a lot of people believe) that Damo imparted on the Shaolin disciples was different to the static and sedentary method meditation that was the only method practiced widely at that time. This ideological framework of physical exercise was ideal for former soldiers/warriors to use in maintaing the similar level of physical discipline that the soldiers were used to. If you think about it, monastic discipline and military discipline are different only in kind, but not degree. Thus physical exercise that incorporated potential fighting applications was introduced. Coupled that with a psychological framework of warriorship in the form of Chan (and later Zen) Buddhism and you get a fertile ground in which what we now call martial arts can grow. Obviously people have been fighting each other for longer than we care to remember, so fighting skills have been in develpoment for a long time. I would say thoug, that up to then these fighting skills were more martial systems and not necessarily martial arts as we think of them today as physical paths to betterment and enlightenment. This is what was unique about Shaolin, not that all of kung fu originated there, which is hogwash.
As for which came first, fist or weapon, let’s take a quick look at an art, Hsing Yi, as an example. The movements were based on spear fighting motions, and the techniques and principles reflect that. So in this case we have an art where the peaon came first. OK, what about another old art, like Suai Jiao? Well as a grappling art this is a development of old-time wrestling harkening back to the days when we were just crawling our way into sentience. This is an art that not necessrily grew out of weapons skills. But we should also acknowledge that both these things occured concurrent with each other. Meaning that the spear guy probably learned to use his weapon so he could fight anybody, where it was another spear guy, sword guy, or a shuai jiao guy, and the same for the wrestler. Once we got sophisticated about learning to hit and kick more efficiently, then the two processes fed off of each other.
So in conclusion I’d say if you go far back enough, it’s like the question of chicken or the egg. When we are talking about codified martial systems it may be easier to determine from what source a particular system of fighting may have found inspiration, but that would only be true within the last 2-4000 years - within the written historical period. Much of Human history is unwritten and far deeper.
What we do in life, echoes in eternity
–Maximus Decimus Meridius, General of the Army of the North, Commander of the Felix Legions