Interesting idea.
However, might be much faster and more convenient to temporarily install self contained CIWS per RORO ship, and a datalink to other surface platforms and/or shore based MALE and HALE surveillance drones.
There are tradeoffs.
Every shooter platform requires field of fire control. The more such platforms you have in close proximity, the harder that becomes.
Even with self-destructing ammo, having a CIWS will require you to space out you merchant ships 2~3,000m apart - more if you don't trust the confluence of Murphy's law and the dud rate on the SD ammo. Putting each vessel 3,000+m apart really spreads out your fleet, increasing the difficulty of covering your invasion fleet with the next layers of short and medium range AD. You could pack them closer but then you'll need to be very accurate on arcs of fire and station keeping, having small crews on board each civ ship to service the CIWS lest they flip the thing to the wrong mode, etc. Complications -> Murphy's Law.
The other method is the traditional convoy and escort method. Pack all your civvies in a herd and put your watchdogs in between them and the likely incoming vector(s). Allows you to pack the civvies closer (100m spacing) which condenses the area your layers need to cover.
There are 2 things that are inherently difficult in this environment that a lot of non-prof seem to take for granted. Within the military, there are a lot of compartmentalised networks both intra- and inter- unit/formation (let alone inter-service). Comms across multi-service, large ops is never easy and relay lag is a real thing even if the signals themselves are near instantaneous. Better to shorten the loop in the case of dealing with inbound bogeys where your engagement window is under a minute.
The other stems from above, which is blue-on-blue. Everything needs to be deconflicted - from the channels that your naval gunfire support (shells) flies through to the lanes your air assets ingress/egress, everything needs to be accounted for. The sea might seem like a big place but it can get incredibly crowded when you have an invasion fleet of a few hundred vessels. Even if you have SD shells, a dud rate of 1% can mean an awful lot of strays in the beaten zone - and generally, in an amphib scenario, where the incoming bogeys are coming from is the same direction as your LZs are, so guess where your beaten zone is?
Which is why (coming from a TAG background), the idea of thousands of FPV drones swarming the area I'm in, controlled by operators 10s of km away with no direct comms, looking for targets of opportunity? I'm crawling into a bunker till they go away - in between low fidelity optics, EW degraded signals, opstempo hastening their decision making - I'm not taking my chances. Battlefield Management Systems do make things a little easier but really, target id is not as easy as you think it is, especially in the world of those guys behind enemy lines doing blocking, interdiction and just generally f-ing with the enemy's rear (sometimes driving commandeered vehicles as well). I'm not coming out until someone
deconflicts my battlespace.
