Are there other examples of naval bases being deliberately situated in shallow-water harbours post-1801?

Not an answer by itself - but an explanation of the trade-off against vessel draught when selecting a harbour.

First, the distinction between a port and a harbour:

• A port comprises the (always man-made) facilities for loading and unloading both cargo and passengers/crew from a vessel.

• A harbour comprises the facilities (always at least partially natural though now often enhanced by man) in which vessels can seek haven from inclement weather, be stored awaiting use, and await turn for nearby port facilities.

That said ports, and in particular large ones, are nearly always located in or in very close proximity to harbours, for obvious reasons. So the question really should be phrased as

Were military ports ever deliberately situated in shallow-water harbours post 1801?

However that is clearly the intent of the question - so we will continue.

Now the trade-off; In order to anchor securely a boat must feed out sufficient scope (nautical: The length of cable extended when a ship rides at anchor.) of anchor line (often estimated to be 8 times, or even 10 times in bad weather or waves, the water depth. Here, water depth is the height, at high tide and including maximum expected wave height, of the anchor line hull attachment above the harbour bottom.

In consequence of the greater scope required in a deeper harbour, vessels will also require a greater radius of free movement. In particular this radius of free movement must be clear:

• of all water that might beach a vessel; and

• all other vessels also at harbour.

Some mitigations are available as regards minimizing interference with other vessels:

All vessels in any harbour must abide by the anchoring rule for the harbour, namely:

• one point anchor only; or
  If all vessels use one point anchor only then they will allowing free in roughly the same direction due to tide, wind and wave action, though minimum clearances must still be planned and abided by. All vessels will naturally swing to point into any wind, wave, or tide that is exerting a sideways force on them, minimizing any tendency to pull anchor, so a minimum scope may be used.

• two point anchor only.
  If all vessels use two point anchoring then they will not swing, and thus will not be able to minimize sideways wind, wave, and tidal action. So vessels may be anchored closer together, but will require additional scope to reduce any tendency to pull anchor in inclement conditions.

An aside: In my Cruise Yachting course many years ago, it was repeatedly emphasized that all vessels arriving in an unregulated harbour must seek guidance from a vessel already at anchor, if there is one, as to the anchor rule in use by that other vessel. Failure to either do so, or abide by the guidance received, would of course invalidate any maritime insurance coverage should an incident occur. Only in the happy instance of there not already being a vessel at anchor may a captain choose which anchor rule to use. If one anchored overnight with one rule, then went for a day sail returning in the evening, always ask again because there might have been complete turn-over and a new rule in place.

Finally, the nature of the harbour bottom itself is likewise a primary consideration. A harbour bottom unable to hold anchors in inclement conditions is a bust - so one might choose a shallower harbour with a good bottom over a slightly deeper one without.

So yes, there definitely is a trade-off where too deep a harbour is disadvantageous. Too deep a harbour will reduce the maximum number of vessels which it can house at any one time in safe anchor. Further, in a harbour of varying depth, there is great value to clustering shallower draught vessels in the shallower water and only deeper draught vessels requiring such in the deeper water.