What therefore confuses me is how do the Reapers have such great numbers, if each Harvest has them loosing more ships than they started with? Do they re-build the destroyed Reapers after they're done?
Yes they have a lot. I would also include processing ships and troop transport ships. The scene showing the reapers approaching the Milky Way, after the suicide mission, shows what looks to be processing ships and troop transport ships along with other reaper ships
A post on the first page mentions that Casey Hudson says that only a few destroyers are lost each cycle while one capital ship is lost every few cycles.
I will use the number 3 to represent few.
That means that 6 667 capitals ships have been destroyed if I use the 50 000 year cycle over 1 billion years and 60 000 destroyers are destroyed in the last 1 billion years.
So when the reapers arrive at the beginning of our cycle they have about 13 333 capital ships plus destroyers, processing ships and troop transport ships
Of course I have no idea how long the 50 000 year cycle has been happening. Leviathan mentions that the intelligence directed the reapers to build the relays so the number from above most likely would be lower. If the reapers have been around longer than 1 billion years, then the number above most likely would be higher. At the moment its just guessing until Bioware says how long the 50 000 year cycle has been happening
With that many destroyed over that period of time I would say more of them would've been discovered in space. As far as I know the only two that are discovered is the one the Batarians found and the one Shepard boards to get the IFF.
Here's some possibilities. The reapers destroy whatever is left of the dead reaper so no one will find it and study it. The reapers reuse them to replenish whatever losses they encountered during the harvest. Or they could just rebuild the dead reaper
Lets say Shepard picks refuse letting the reapers harvest us. It would take them a fair amount of time to replenish their losses.
If using the 13 333 number from above, there is no way we have a chance to defeat them without the crucible. Had the reapers not been stupid in ME3, the crucible wouldn't of been built. With that number the reapers have, the only way to defeat them is to find the plans for the crucible, build it and then use it before the reapers enter the galaxy