There are a few different things to look at.
Take a look at Hondas factory racebikes.
Nearly all of them had the same number exhausts as cylinders.
Some of the advantages to this design are:
The ability exactly tune the the exhaust to engine performance, without dealing with a collector and the pulses and exhaust of the other.
The ability to quickly diagnose a mixture or other problem with a given cylinder
Awesome sound
Disadvantages:
Weight
Cost of materials
4 into 2 was a popular aftermarket design for the SOHC4 CB's
Some Advantages
Still easier than a 4 into 1 to design for pulse and exhaust evacuation, assuming 1 and 4 are on the same collector, as are 2 and 3 on their own.
Weighs less than 4 into 4
Somewhat easier to diagnose issues by exhaust characteristics than a 4 into 1, at least by narrowing down the conjoined cylinders
Disadvantages
Many 4 into 2's have 1 and 2 on one and 3 and 4 on the other. This creates an unequal pressure and pulse signature, and one pulse will have better exhaust evacuation than the other in this configuration.
Many of the aftermarket 4 into 2's were low and would scrape.
Still heavier than 4 into 1's
4 into 1's are very popular, and were stock on the "F" model cb400's, 550,s and 750's.
Some advantages
The stock really wasnt much lighter than the earlier hm341's and hm300's, but the aftermarkets are pretty damned light
A properly tuned one will still evacuate exhaust very well, using the inertia of the last exhaust charge to pull out the exhaust evacuation of the next cylinder.
Most are turned up well and give good ground clearance
Usually much lighter than the other configurations
Disadvantages
Poorly designed ones are not setup to help evacuation at RPMs you might want to run at
Removal and reinstallation of headers can be a pain in the ass on some designs
