Thanks everyone for the help. I will post back here my findings.
I've discovered that the slowdown was caused by me keeping everything on USB disk! I had my Wii games, GC games, apps (ULGX, emulators, etc) and emuNANDS all on the same USB disk, with nothing on SD Card. This was brilliant from a portability aspect, but it slowed things down. It was bearable before I installed Wiiware to the emuNAND, but once I had loads of Wiiware channels installed it drastically slowed down ULGX and made the Wiiware unstable, often they would struggle to save and then crash.
Just moving my 10gb Channels emuNAND to SD Card was enough to fix it. I haven't tested with a larger emuNAND, but the size seems less important now.
Why would this happen I don't know, as in theory USB should be faster than SD? Maybe the USB connection was getting overloaded, whilst having some stuff on SD helps relieve the bottleneck? Maybe there is a bug in uneek that isn't in sneek?
Anyway this is what worked for me.
P.S. As it turns out Wiiware and VC games are a real pain! Only about half work straight away for me, so it means a lot of fiddling with settings and running some in full neek mode. It's not like this with Wii games, the majority work straight away, with only a few needed some adjustment. It's a pity there isn't a definitive answer of which work and which don't, then I could simply install the working ones. Someone kindly created a compatibility list, but it is sketchy and incomplete. I can't be bothered to fiddle around with all my 600 Wiiware and VC games, so I've abandoned the whole thing and given in, to save my sanity! Maybe I will revisit it later, in which case I will post more info here.