That is true AndrewW, but if you have a 200 Far trader type A2 with Jump 2 specs you have 15 tons of Drive costing 22.5 million Credits. There are 64 tons of cargo space.
If you take the 10 percent disadvantage your engines now take up 16.5 tons and cost 12.375 MCr, a savings of 10.125 million credits.
For Jump Drives:
Assuming you took the 1.5 tons of space from cargo the A2 now has 62.5 tons of cargo space instead of 64.
Income from freight shipping for J2 is 1600 per ton, so 2400 lost credits in income per trip, meaning the break-even point is 4219 trips, about 162 years at 26 Jumps a year, if all you do is ship goods. Spec trading may reduce that time, especially if you have a good broker skill.
So the cost reduction is very cost effective for what you lose and gain.
Power Plant: Increasing size for the A2: 5 tons of plant worth 5 Million
You get 5.5 tons of plant worth 2.75 million. The 2.25 million savings is worth half a ton of shipping space (800 credits a trip), 2812 trips, or 108 years of savings.
Decreasing the size by 10 percent and increasing the cost by 50 percent means a 4.5 ton power plant costing 6.75 Million credits for a space increase of half a ton. In shipping terms that means a payback in 324 years.
If you have the volume available it pays off to increase the size of your gear. (when compared to the income loss from freight shipping, but unless you are speculating on tons of anagathics or million dollar exotics the payback time is pretty long)