Sure the 90cc pipe will work. It will direct the exhaust gasses away from the engine just like any other exhaust pipe. You might even get a power boost from it at some random rpm range. However its not designed for that specific 50cc engine. While designing the pipe, just about every aspect is determined with an equation. The "Best" pipe(ridiculously broad term) would be one designed for your engine, and what you want your engine to do.
Header - Attaches to the engine and is the straight or slightly divergent (opens up 2-3 degrees) section of the pipe. It helps to suck the exhaust gases out of the engine. The header pipe cross-sectional area should be 10-15% greater than the exhaust port window for when maximum output at maximum RPM's is desired. In some cases the area of the header pipe may have a cross-sectional area 150% of the exhaust port area. The length should be 6-8 of its diameters for maximum horsepower, for a broader power curve 11 times pipe diameter may be used. The part you trim off to tune.
Divergent (Diffuser) Cone - The section of the pipe that attaches to the header and opens up at an angle like a megaphone. It intensifies and lengthens the returning sound waves thus broadening the power curve. The steeper the angle the more intense the negative wave returns, but also the shorter the duration. The lesser the angle, of course, returns a less intense wave, but for a longer period of time (duration). The outlet area should be 6.25 times the inlet area. 7-10 degree taper angle.
Belly - Located between the divergent and convergent cones, it's length determines the relative timing of the negative and positive waves. The shorter the belly the shorter the distance positive waves travel and the narrower the RPM range. This is good for operating at HIGH RPM only. The longer the belly the broader the RPM range. The diameter of the belly has little or no effect.
Convergent (Baffle) Cone - Located after the belly and before the stinger, reflects the positive waves back to the open exhaust port and forces the fresh fuel mixture back into the combustion chamber as the exhaust port closes. The steeper the angle the more intense the positive wave and the gentler the angle the less intense. 14-20 degree taper angle. The taper angle primarily influences the shape of the power curve past the point at which maximum power is obtained.
Stinger - Located at the opposite end of the pipe from the header and after the convergent cone, it is the "pressure relief valve" of the pipe where the exhaust gasses eventually leave the pipe. The back pressure in the pipe is caused by the size (diameter) or length of the stinger. A smaller stinger causes more back pressure and thus a denser medium for the sound waves to travel in. Sound waves love denser mediums and thus travel better. A draw back to a small stinger is heat build up in the pipe and engine. The stinger diameter should be 0.58--0.62 times that of the header pipe and a length equal to 12 of it's own diameters.