I say that HDD speed will make SOME difference in Amiga, you need to consider that most of Amiga software/games are about 2Mb in size, and most of things are really, really tiny (kb).
So, if you have transfer ~1.5 Mb/s (standard speed for A1200) and then later 8Mb/s (FastATA), there is SOME noticeable difference. HOWEVER, for Amiga the biggest difference you will see is after installing CF memory instead of HDD, since access time to files will be instant.
If you change regular HDD to CF in plain A1200 and install system on both without anything, you will see that Amiga with CF boots literally INSTANTLY (no HDD start etc.). Regular HDD and CF easily "saturate" IDE port in any Amiga.
HDD speed in Amiga is not that important (if you have CF memory as HDD). You can have super nice hard drive and it will take few minutes for 030 to show you a high resolution picture

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If you get 16.6Mb/s on regular IDE port in Amiga I will eat my shoe

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