These are good observations. What about if you're explicitly not shipping all the code to each client, but have individual projects per client? Some of these criticisms still apply, but it seems more natural to have a repository per client/project when you're building bespoke solutions, or customizations from an inventory of shrink-wrapped solutions. [And clients must only see their own code.]

If the problem is the usability of multiple repositories, could this be solved with better tooling? Projects like GVFS suggest that monorepos do not avoid a need for strong tooling.