No. qPCR is, well, quantitative, so it gives more information. Additionally, it requires less pipetting, and the data is easier to report. All of these things make it more desirable for diagnostics.
In general, titers of the virus in NP swabs should be high enough to withstand 10, maybe 20-plex pooling. However, as you allude to, there are plenty of other effects that can influence PCR. If there is one sample, for example, that contains a PCR inhibitor, like heme, it may then inhibit all the samples it is pooled with.
Additionally, swabs are not just swabs of virus, they also pull of highly variant amounts of bacteria and human material. These things may also affect the efficiency of PCR.
Pingu is also very good. If you haven't seen it, it's a Claymation penguin and his family. He's not a goody goody--on the one hand is just funny, but on the other hand it gets to explore his kid-life and kid-choices. TH other fun thing is, they all speak a language made up by the Italian opera singer that voices them.
If you look at it another way, groups that have a handle and understanding of a particular tool may have insight into how that tool can be used to answer a biological question. I don't think there is anything really wrong with that, but grants should be denied if they aren't proposing ways to move the field forward.
There are tons of mouse labs, however some have specialized mice or mouse systems. There are also other labs that specialize in other animal systems. These systems are nontrivial to switch between for many reasons, which I think you acknowledge. It is useful for the field in general to have access to the results of a variety of research tools that every individual wouldn't necessarily have access to.
