Why would you need an "electric distributor"? In fact what is an "electric distributor"?
It would also be very helpful if you told us a little more about what exactly you're starting with - a 1988 what with a carb 1.3 - and maybe where you are, because whatever it is, it more than likely shipped with different configurations depending on the market it was built for.
A carbed vehicle can have either an old school breaker point ignition system, or electronic ignition in which the distributor contains an igniter that switches the coil (which, by the way, is what a US market 88 Samurai would have had) - either style can probably be used to trigger your megasquirt for both injection & ignition, assuming you're going to run single point injection or batch fired multi-point injection - if you want to control the ignition advance with the megasquirt your can either lockout the advance mechanisms on the distributor, or use the distributor only to distribute the spark and trigger the injection & ignition using a pickup and a trigger wheel mounted on the crankshaft pulley - using a trigger wheel has the advantage that you can probably use it to control sequential fire multi-point injection.
On to your last question - as far as I know all the distributors that Suzuki used with the 1.3 & 1.6 engines were electronic (ie. no breaker points) and as to whether a 1.6 distributor will fit and work with a 1.3, that's going to depend on the vehicle the engine is in - some interchange some don't.