I've been going back over some material on the sixth-century plague in the past month or two, partially for another project (digital textbook), partially for this new (ish) research project, and partially out of interest. I've made Meier's new article (Early Medieval Europe 2016) bus reading, and so I've been slowly working my way through it, and definitely enjoying it. My bus trips are short, so I only ever get so far.
So far, just over halfway through, I think he's done a good job of summarizing earlier research - it's an excellent introduction as is to the subject - and is making some good points all the same. Earlier today, I came across his brief sections, lines even, on the effects of the plague on waging war. As he notes, this is an issue that hasn't been resolved.
Some hold that the plague had a significant impact on Rome's ability to wage war, let alone that of other states like Persia. This impacted everything from financing war to the paying of troops. The varied instances of military unrest that cropped up afterwards in places like Africa should be attributed to the lack of money to pay the men. Problems with recruitment too - Belisarius had to rely on finding men himself later during the war in Italy - would also come down to the impact of the plague. There simply weren't enough men.
Others, however, hold the opposite line. Rome was able to wage war on at least two fronts simultaneously during the outbreak of the plague, which would seem to minimize its impact on the empire's ability to wage war. The thinking goes: if plague really did have a significant impact on Justinian's military, how could they put 1000s of men in the field in Africa, Italy, Bulgaria, and Syria at the same time?
As noted, this is an issue that hasn't been resolved, and it's one that's interested me for a little while. Coming back to it again now, however, is it even possible to get any kind of resolution? Most importantly, how could we hope to measure the plague's direct impact on the state's ability to wage war? Our evidence isn't good enough, so far as I can tell, to indicate changes in the number of soldiers fighting for Rome before or after the plague took hold. There are a few big figures for the military as whole, and references to various armies by Procopius and others. But those are very much context specific, and there's often a lot of material that gets left out.
We also know little about the specifics of recruitment. There are a few pieces of legislation that get into recruitment, and some of this we can date with a good deal of precision. But the recruitment material is from the years before the plague broke out. It also tends to be about the process itself: these are the sorts of men who can and should be recruited, and this is what they should and should not do. It doesn't reveal anything, really, about where they might be from and what to do if men couldn't be found. There's no legislation that reveals any sort of crisis in recruitment in the middle years of the sixth century.
The truth is, the evidence, as a whole, is often ambiguous. While it might reveal things like damage, depopulation, financial instability, and mixed success in war, it doesn't connect these potential impacts of war to the wars themselves or the plague. For instance, was the Roman Empire in the 540s and 550s struggling in war so much because of the plague, or because it was engaged on so many different fronts? To take another example, Procopius spends a good deal of time on the impact of the plague on the empire in his famous passage. He also details the impact of the wars in his Wars and Secret History. What he doesn't do, however, is connect the plague to the mixed success at war. It could be because there was no connection. It could also be that he didn't realize that there was a connection. Or it could be that there was one that he recognized, but one he chose to ignore in favour of other explanations, like the evils of Justinian.
In short, there's no resolution yet for this problem, but I'm not sure we could ever get a definitive one. With that said, the best, I think, that we could hope for is an analysis of the indirect or circumstantial kind. There seems to be better evidence for the impact of the plague on other aspects of life, like the broader economy and rural agriculture. If we can establish its impact on all these other matters, it seems likely that it would have had an impact on the military too.