That is likely the truth, Keith. Practicality and financial sense has always been at the top of the list for any redevelopment, and perhaps rightly so as without a business case it's not getting done.
Additionally, 'recent history' has little value when work has to be done, and items such as those stone markers would not have been regarded as significant once they outlived their usefulness as actual markers. Besides, they would have been heavy to remove and they would make great fill.
From what I've read, it has only been in the last 40 years or so that any kind of urban archaeology has been done in Halifax when an old site was redeveloped. There were many developments done before the 1980s where old buildings were torn down, a hole was dug, and any artifacts that might have been contained in the removed material were hauled off and dumped unceremoniously at another location, whether as fill or otherwise.
Over the passage of time, however, we (a generalization) have realized the value of researching our own history, and thus have decided to put rules in place such that historical sites like this require some archaeology before construction can begin. So, what was once probably considered excellent fill material will now be displayed as a link to the site's military past.
But, yes, I think in general our forebears were simply concerned with survival and getting things done, and didn't take great pains to try to preserve such things.