i've done the same thing to my z750 stock exhaust. it IS louder, but the sound isnt very nice, if youre only looking for loudness then u can do that, but it isnt very... growly... sounds a little like a fart can i think lol
if u dont want to spend too much on exhaust, i guess you can go for Danmoto exhaust, i got their carbon GP a while after drilling my stock, it works wonder, looks decent, been using it for about year and a half, not a single problem, but i would recommend you to get the baffles as well cuz it is REALLY loud. i decided to order the baffle after using it for 2 months. and you do get a little low-end power back with the baffle.
here is a link for exactly your z1000:
Z 1000 2003-2006 Carbon GP [EX-00019] - $245.00
and this is the picture with them on the z1000
i think they look nice
and at $245... ehh not bad for 2 pipes right?
there will be people telling you not to get danmoto, but imho this is worth it
PS: i've heard ppl complaining the rubber mount on their metal danmoto pipes melting, the carbon ones don't have this problem cuz carbon doesnt conduct heat as much as metal, i can touch the carbons on my exhaust without burning after riding, this helps passenger from burning their feet by accident i guess.