Getting results without using IN Oracle has a limit on the arguments in the IN statement of 1000, I believe, is there a way around this? If I had a statement similar to this (with 1000 ids or more):

SELECT COUNT(*) 
FROM "VERSION" 
WHERE "VERSION"."VERSION_ID" IN 
      (59156, 57045, 54779, 54048, 54048, 
       --- long list ---
       12648, 11160, 11160, 11160, 11160)


How could I write simple count statement?
Try creating a temporary table to hold all of the IDs you want to search on then join in that temporary table. 

create table tmpIds(id int not null)
insert into tmpIds (59156)
insert into tmpIds (57045)
etc...

SELECT COUNT(*) 
FROM "VERSION"
INNER JOIN tmpIds ON 
"VERSION"."VERSION_ID" = tmpIds.id

drop table tmpIds