it took me up to 1'30 to count a relatively normal position when I started. With practice I got to 45'' for a simple position, but in any case this still feels like too much in a normal KGS game (I usually play 30'+5x30'') even if I'm a fast player.

45 to 90 seconds for a fresh count of the whole position is great for your level. I am not faster (but more accurate and familiar also with counting complicated positions).

Of course, a player cannot spend 45 or 90 seconds at every move to count the whole position from scratch. This is where the techniques of the chapter for updating counts come in: during most moves of the game, one should update the count instead of counting the whole board again. Updating is fast: it takes a few seconds or sometimes only fractions of a second. Only occasionally a new whole board count becomes necessary. Learning to update counts takes some time of gaining experience.

KGS games tend to be fast, and such fast games are not so suitable for learning and practicing counting. Nevertheless, your 30 minutes basic time can suffice, if you learn to update counts regularly by recalling which intersections are the territory intersections etc. OTOH, you might try 45 or 60 minutes basic time as long as you still learn counting. When you will have become familiar with performing it using updated counts, you can then go back to shorter thinking times.

Counting in byoyomi-only games is even much tougher, but possible, if one starts updating counts from move 1 of the game. Of course, I do not recommend pure byoyomi games for learning to count well.