Can I remove unneeded 2 plugs from PCI-E power cable?
You can remove the unneeded connector and conductors. However, in the event that you end up needing an 8 Pin PCI cable in the future, you may regret it. You may also damage the connector in the process.

Pins are spring loaded and the usual process for removing them is to use a proper size pin extractor. Inserted from the pin side, the extractor consists of a sleeve which slides over the pin and folds the locking wings back into the pin. A plunger on the tool is then pressed which goes through the center of the pin and pushes it back out of the housing. These extractors come in different sizes and are about $10 or so.

In this case I really think you are better off leaving the cable assembly as is.