I am able to suppress the exception by using following;
num = NumberSeq::newGetNumFromCode(<<someNumberSequenceCode>>, NumberSeqScopeFactory::createDefaultScope(), true, true);
As, fourth optional parameter of NumberSeq::newGetNumFromCode(,,,true); says not to throw exception on missing reference.
boolean _dontThrowOnMissingRefSetUp = false,
As I said earlier, I have created number sequence from organization administration without writing any code (EDT, class, parameters table etc. stuff) so no reference was generated and I think I was getting exception due to this.