@wawrzon
Please dont compare it with OS4, as it is totally unrelated and bloated compared to original AmigaOS. For example, you need at least 32MB of ram just to boot!
On my 3.1 setup, which includes a custom built rom, my boot time is about 15 seconds or so, and it is an A1200 with a 68030, nothing too fancy, and using just its internal IDE port.
There is certainly something wrong (or highly inefficient) with your current 3.9 setup. Watch the video (he is not using a rom based kickstart, so your times should be even better)
https://www.youtube.com/watch?v=32DHRlBWKs4