So guys after almost 10 days of life and self fixing, i just finally resolved the problem at least of course on this machine, and: it WASN'T nothing related to the SB Live! drivers or else.
The real problem was.......the USB. Yep. I don't know how, as usually when my 6th sense tells me to do something, i just figured out as i was trying to fix another annoying problem: playing some old adventure games like Monkey 1 and Simon The Sorcerer on MS Dos mode, everytime i moved the mouse the music and game drastically slows down. It was really annoying, i searched on net and i've tried three different CuteMouse drivers from 1.9 to 2.4 beta. Even a Mouse.com driver i found on an old my floppy disk. Nothing.
Then, out from nowhere, i tried to completely disable USB support from BIOS (which is already itself very limited on this board), disabling the 1.1, 2.0 and legacy support. And BAM guess what? Now Win98 correctely shutsdown everytime and reboots just fine without the need of any patch or leaving my SB Live! card and drivers untouched. Top of that, even the mouse movement lag disappeared.
I don't really know how this is possible as the SiS drivers were installed and worked just fine with all ports and usb sticks i've tried, but somehow looks like this was the real problem. The new one this, is that i use really often USB because with my 16GB FAT32 stick, i always move new games or files from main modern PC to this, so now everytime i will have to enable manually on BIOS, use it, reboot and disable it again. Annoying, but at least i can shutdown and no more lags.
I think my only explanation on this case, is that I noticed when i leaved enabled all three USB options on the BIOS, in the menu of IRQ's right before Win98 starts to boot i saw there are a lot of IRQ in the list, which some are "NA", and from Win98 device manager there are like three of them all looks alike between them, and they are using resources like IRQ 3,4,5 which are vital for SB Live for example. But even disabling them or change manually the IRQ from device manager, didn't do much at all so the only way is to disable completely under bios and this fixes the shutdown problem, despite of course i can't use any USB sticks or device now.
Thank for all help and hope this could help someone!