Ah. When you said level 30 before, I thought you meant upgrade levels. Difficulty level 30 (or 40) is very different. :-)
FWIW, the Bonus upgrade doubles the bonus number that you see in the upper left corner while you're playing. The bonus is used in calculating the points you get for each kill, so the upgrade increases the number of points you get, but the effect is kind of hidden.
Before that upgrade, the bonus at the beginning of each game starts as the number of achievements you've earned, and 1 point is added to the bonus for each wave (after wave 1) when nothing gets through (ie. you don't lose any health). With the upgrade, the bonus starts as twice the # of achievements, and you get 2 points added for each wave when nothing gets through.
Note that if something does get through, the bonus gets reset to the starting number, so having something get through later in the game can really hurt your score. And having things get through frequently can just kill it, because the bonus keeps getting reset to the starting level.
Since the starting bonus is based on the number of achievements you've earned, working on some of the easier achievements can help boost your score.
As for what to unlock next, it may depend on how you play. There are some things for specific types of towers, like AA cannons or mortars, so one of those might be good if you use those towers a lot. If you sell towers a lot, the one to get more money when you sell towers might be good. Personally, I've never found the mines or flares to be very useful, but flares might be more effective at a lower level, like you are now, so I suppose those might be worth a look.
If none of those special upgrades seems particularly useful to you right now, just concentrate on upgrading your towers, so you can beat higher difficulties and make more points.
FWIW, here are a few basics about the score:
If you make it through wave 100, you get some bonuses.
The Victory bonus is 20% of your score (the first line).
The Money bonus is the money you have at the end times the difficulty, times 2. So, if you have $50 at the end and you were playing difficulty 30, the Money bonus would be 50 * 30 * 2, or 3000 points. Some people will sell off towers during the final wave, to increase that bonus.
The Remaining Health bonus is a % of the score, where your remaining health is the %. For example, if you finish wave 100 with 25 health left, that's a 25% bonus.
If you don't lose any health, you get the Perfect bonus, which is another 20% (like the Victory bonus).
Hope some of this helps.