Long answer:
CC is the volume swept by piston when it moves inside the cylinder in cubic centimetres. Larger the volume swept, larger is the quantity of airfuel mixture taken in during the inlet cycle, and therefore, higher amount of energy generated, leading to more power. This is why mostly the CC number and the power (PS) number seem to be directly related.
Now, the stroke volume is only one of the few things that determine the power output of the engine. Some of the other factors I’ll discuss below.
CC has pretty much nothing to do with top speeds. Top speeds would generally depend upon the power delivered by the engine(which depends upon the design of the engine) and the weight of the bike. The Duke is designed for speed, the Bullet is designed for pride
Storke ratio:
This is the ratio between the stroke length(basically the ratio of length of the relevant part of the cylinder) and bore diameter(diameter of the piston) are three kinds of engines,

length~=diameter => Square engine

length<diameter =>oversquared engine

length>diameter =>Under square engine
An over squared engine has to cover smaller distance for every stroke, which means it can have a higher number of strokes per minute. This implies a a greater number of cycles per minute. What this translates to, is an engine that is designed to operate at higher RPMs. Or higher speeds. KTM duke falls under this category. Bore to stroke ratio of KTM Duke 200 is 72/49. Most racing bikes and cars use this configuration. Possible downside could be the high amount of wear and tear, higher temperatures and heat loss.
An under squared engine has a longer stroke length, which means it can do fewer cycles per minute, and therefore, lower RPMs. This means it will deliver its peak power at lower speeds(RPM). The royal enfield Bullet belongs to this category, at a stroke ratio of 70/90. Will last long, but if speed is what thrills you, get something else.
Gear Ratio:
The ratio between the RPM of the engine(not really it is actually the RPM of gear primary drive as far as I know) to the wheel. For the bullet, the peak ratio is 1:1. Whereas for the Duke, it is .917 (the wheel is faster than the engine). This implies further increase in top speed.
Compress Ratio
Compression ratio is the ratio of the volume of airfuel mixture before compression and after compression. Higher compression ratios imply higher thermal efficiency, which means higher power output. The Duke has a compression ratio of 11.3:1. The bullet trails behind at 8.5:1.
Weight/Bulk:
In addition to these, the Kerb weight of KTM duke is 136 Kg. The Bullet is a lot bulkier at 187 Kg. Since acceleration=Force/mass, duke manages to get that extra inch of speed by sheer weight reduction. The downside for duke here is the stability that it sacrifices to a certain extent.
All the factors considered, Duke 200 delivers more power than a Royal Enfield Bullet 350, but lower torque, and is faster.