It will waste some space. Small files will always consume 512K regardless of their actual size, which for a single file is quite a lot to loose when you think of the 10's of thousands of small files in the OS and random programs you install. Its a big enough SSD that a wasted GB isn't going to be too terrible however so I wouldn't worry too much about the space cost.
Performance wise I don't know if the controller is smart enough to realise the sector is empty and not write it all when the file is small, my guess is that it isn't and hence you are also getting extra bytes written on small files as well. Most SSDs are optimised for 4k clusters but at the same time they dont work well with 4k since their minimum wipe is larger than that, to some extent 512K clusters might make the drive run faster. Run CrystalDiskMark 3.0.1 c in x64 with 3 runs and 500MB file and compare to the following (we have the same SSD):
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CrystalDiskMark 3.0.1 x64 (C) 2007-2010 hiyohiyo
Crystal Dew World :
http://crystalmark.info/
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* MB/s = 1,000,000 byte/s [SATA/300 = 300,000,000 byte/s]
Sequential Read : 511.085 MB/s
Sequential Write : 266.610 MB/s
Random Read 512KB : 435.377 MB/s
Random Write 512KB : 268.240 MB/s
Random Read 4KB (QD=1) : 20.381 MB/s [ 4975.9 IOPS]
Random Write 4KB (QD=1) : 70.962 MB/s [ 17324.7 IOPS]
Random Read 4KB (QD=32) : 204.791 MB/s [ 49997.8 IOPS]
Random Write 4KB (QD=32) : 235.603 MB/s [ 57520.1 IOPS]
Test : 500 MB [C: 53.3% (254.1/476.8 GB)] (x3)
Date : 2012/07/22 12:04:38
OS : Windows 7 Home Premium Edition SP1 [6.1 Build 7601] (x64)
Using a bigger than necessary cluster size on your disk will waste some space, but I would like to see your CrystalDisk results as I think it'll change the performance characteristics a reasonable amount from the norm. It might also be reducing the life of the SSD a little bit but nothing to be worried about.
You should only use big cluster sizes when you know the majority of files will be large, in those cases with large media files and images there is a moderate speed improvement and a small saving of space as well.
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