From what I've seen of cruising people that venture into Indonesian waters they have had no more problems with Indonesian harbour masters than with any other harbour master. The trick is to be polite and courteous at all times, have all your paper work up to date in triplicate (at least) with lots of rubber stampings on it, they all love officialdom.
Depending on where you are thinkging of venturing it may pay to keep an eye on this web site for their weekly around the world update on piracy ...
http://www.oni.navy.mil/Intelligence_Community/piracy.htmCatamarans in SE Asia are usually very expensive and few and far between and trimarans even more so.
Some of the local used boat dealers in the area are :-
In Phuket
www.leemarine.com/In Langkawi
www.langkawiboatsalesandservices.com/en/yachtbroker-charters.com/pippenmarine.com/Singapore
www.simpsonmarine.com/en/