I recently did some research on this topic because I want to install an SSD in my Macbook as well.
In my case it would not be a factory fitted one but I doubt that there are big technical differences between original Apple SSDs and custom ones, apart from TRIM being available by default vs. enabling TRIM on my own with a custom SSD.
The most satisfying answer I could find was this discussion in the Apple Support Community.
The interesting posting basically says that a user tested random sectors on a FileVault2 encrypted SSD and found some that were indeed empty (all zero). In a similar scenario on a classic magnetic HDD no empty sectors were found.
The user concludes that this means that unused sectors remain empty on SSDs and that TRIM will correctly work with FileVault2.
The conclusion seems reasonable to my understanding and after installing my SSD I personally will use FileVault2 in good conscience.
However, this is not an official answer from Apple and therefore should be treated with care.
I have the same problem, which I'm pretty sure is due to a combination of the way write operations work on flash memory and the way core storage (or any whole-volume) encryption works.
First, write behavior: unlike volatile memory (the stuff used in the memory of your computer) or hard disks, where any bit can be written to 0 or 1 at any time, flash memory has two main states: written and erased. Within "written" are 0 and 1. When you need to write to flash memory you must write an entire block that is currently in the erased state. File system software in the OS may know what blocks are free, but the controller and storage on a flash device don't. A special way for the OS to tell an SSD to make blocks available has been devised for "bus-connected" SSDs: it's called TRIM. USB protocol stacks don't, to my knowledge, support TRIM. So, basically, flash memory continues to fill up until there are no actual erased blocks, at which point the file system has to erase and rewrite blocks by reading them, merging in the new data, erasing, and writing them back out. That's why you see small-file write performance degrade on SSDs over time.
The special circumstances of encrypted volumes is interesting: depending on the way the encryption works, it may actually encrypt an entire volume, filling all the blocks with what appears to be random data even if the blocks are actually unused and would contain zeroes. So when you turn on FileVault (or otherwise enable core storage encryption), it basically consumes the entire volume, leaving no space for write operations. The file system has to constantly read, erase and rewrite blocks so that it can rewrite them with any encrypted data you want to put on it.
Now I will say right here that this is speculation based on a reasonable understanding of how things work, but there are people who actually know the details, who may correct or improve my explanation and I hope that they will do so.
Best Answer
Every time you make the computer do something extra, in this case encrypting/decrypting all file access, it will take longer and the machine will slow down a bit.
FileVault 1 did slow things down noticeably, but with FileVault version 2 (Introduced in OS X 10.7 (Lion)) running on an SSD there is no noticeable decrease in reading or writing files. I have this enabled on a 15" MacBook Pro Retina and a 2012 11" MacBook Air. The only time it is noticeable is when you reboot, as it requires a password before starting the boot process.
You may notice that the system is slow when you first enable FileVault 2, since it has to encrypt the whole drive. Once that is done you will probably forget that it is on.
If you decide that you don't agree with me, turning FileVault off is easy enough. You will, once again, have the slow initial period as the whole drive is decrypted.