It's horses for courses I guess. You say that you don't have any damaged or dodgy fonts, but Postscript screen fonts without printer fonts are exactly that - they're dysfunctional, especially when you come to try to print any job containing them, so any font utility will alert you to their presence, but as you may, for some reason, want to keep them the software will not remove them for you.
I think that, because of Truetype and OpenType, editing font suitcases is no longer feasible without font editing software. Many of the anomalies that existed in Postscript have been ironed out with the new formats, and OSX is orientated towards these rather than Postscript, so it's something we have to learn to live with. I used to edit my screen fonts in the 'old' days, and got into countless messes because of it, so in a way I'm glad that ability has been taken away from me.
One thing I have just noticed is that, when an old Quark job is re-opened, FontExplorer Pro does NOT automatically install the true italic or bold versions of fonts which have been italicised or emboldened within jobs, so we still have to manually load those fonts. The other utilities do achieve that, so it's a little disappointing to see that this problem has not been corrected in the Pro version. I hear the purists crying "You should use the true versions of those fonts right from the start", but they're not necessarily my jobs which I have to re-open.