You can think of each altar as producing 1 of the 'shard' resource per turn, the main difference* between these shards and other resources is that your shard count is not cumulative, i.e. it doesn't add up from one turn to the next, but resets every turn. So each turn your 3 earth altars produce 3 of the earth shard resource, and next turn you lose those 3 and your altars generate another 3 (or 2 or 4 if you've lost or gained an altar since last turn).
It's actually not the only resource that functions like this - say food or production are also noncumulative, you get a certain amount each turn which you can either use or waste as the case may be, there's no 'saving' up the extra. From a programmer's perspective, it makes sense to have every resource generated on a per turn basis, and simply flag whether you want them to add up from one turn to the next or reset each time. It allows you to write one piece of code that can deal with any resource, it just behaves slightly differently depending on that flag.
But yeah, from a user perspective, that all probably seems bizarre - it'd be easier to understand if they added a little interface translation to represent 'shards per turn' as simply 'shards'.
*Well actually, there's another difference, shards are not consumed when 'used' by a spell. This is not necessarily connected to the whole accumulation thing discussed above, though. Influence, for example, accumulates from one turn to the next, but it's not always consumed when 'used', it has an effect on the way AIs treat you without being used up - the same way shards have an effect on spells without being used up. So each resource can either accumulate from one turn to the next or not, and it can be consumed when used or not (or both, if it has multiple uses like influence does).
