For myself, the Amiga is as much an instrument as it is a machine for music production. I love the colour it adds to basic sounds. Non linear DAC, quantisation noise, aliasing they all add to Paula's charm.
I've never had any serious latency issues with midi. I expect having an accelerated machine helps. Although I believe the EClock timer should be more than accurate enough.
I've never tried it but I imagine ST emulation might be an option if you must use cubase or similar.