Thanks Kostya, it makes sense but is not what is going on! I turned conversations off when it defaulted on with last update as I don't use them, mostly because I am routinely changing the subject to reflect the content whereas typically people put no attention to this important aspect.
To be clear I don't have to count emails in the Smart Folder, just look at the unread / read counts and add them up to see they don't total to the numbers listed for the smart folder. When I was quoting these figures in my OP they were all read, as having unread ones kinda defeats the point! But all the figures quoted are true - why the smart folder doesn't display all emails remains a mystery and is really a pretty serious nuisance as I was simply unable to find emails I was pretty sure I had seen. Now I know of the problem at least I can work around it by going to the account inboxes and finding them that way.
What I suspect is there is some internal limit that is hit. Right now I have 13 in the Smart folder and that exactly equals the total of the inboxes which are 1's and 2's and a 6. When exactly it starts dropping them out of the smart folder I don't know as I have only just realised it is the app losing its mind, not me. But I am sure it has happened for quite some time across versions of Android and Aquamail, so it is "baked in" in some way. I have been an avid user of the app for at least 2 years.
One possible aspect is I don't clear out sent or deleted messages. Currently showing qtys of 178/35, 3/0, 1/3, 2/1, 8/3, 463/0, 3/0 & 1/1 for sent / deleted respectively. I do use the permanent delete feature, a lot. The 178 is my default account and the 463 is a gmail account.
If there is some diagnostic work I can do next time I notice a disparity please let me know. Please note if you search this forum for smart folder you find other people have asked my exact question (without figures) but the following discussion has not got an answer, so I am certain it is happening, just not sure exactly what the necessary conditions are for the smart folder to stop displaying all emails that fit the criteria.
By the way I tried setting Current month with the figures in my OP but that didn't change the figures at all, which was not surprising since the period I had racked up the then load of emails was all in the current month.