The Cap is a very useful tool for stopping leaks, which can make pipe systems more efficient. The Cap can be destroyed in 2, rarely 1 hits from the Portafab. This is fortunate, as this allows for quick stopping, re-piping and so on.
One common use, for example, is to connect Condensers easily. While using a rotated T-Junction is neater, it takes longer to rotate the T-Junctions, and due to the T-Junction's wideness, there will be no space for other pipes. However, if a Four-Way is used with a Cap pointing away from the Condenser, there is space and everything can be connected neatly.
Some say that the Valve is better for piping systems as you don't have to destroy and place it every time, however, the cap is way smaller, costs less Iridium and the option to turn the Iridium flow on/off is not always needed.