1) I have read somewhere that after 100 transactions the poolkey/adress change in wallet etc... I cant remember the exact name. Does this also effect the paperwallet?
I dont fully understand what you mean by poolkey. Maybe you mean the seed (from which are all addresses generated)? In this case no, this seed remains unchanged for eternity and there is no limit (of 100 or whatever) transactions in single addy, nevertheless its much better to always use new addy.
Could be a problem in future to sent these bitcoins out.
TL:DR - Yes, be aware of this, fee could grow very high (half of balance). Check the formula at wiki/Transaction_fees and read the bold.
I had a same issue in the past ... used single addy for all my mining, testing various pools, companies, buying small contracts .... A BIG MISTAKE.
Had around 300 transactions in single addy, but only 0.02 BTC in total. When i want to send them out, the fee was more than half. Sweep to blockchain.info didnt work (too many transactions).
This was year ago, when BTC price was high, so I was looking for any way to avoid high fee and to take all the coins out took me whole month.
When sending larger amounts you can add these small dust transactions without raising the fee ... like sneak them in.
So whenever I made a bigger transaction (from different addy in same wallet) I add a small amount of BTC (usually sum of 5 or 8 transactions) - you need to have wallet which can do this, I used armory.
This way reduced total number of transactions to less than 200 and then sweep to blockchain.info worked. This all cost me 0.0001 BTC and lot of time.
Is there any downside if you let the pool payout every hour instead of every let say 6 hours? Because I can imagine that if you let payout everyhour, after a month there is a huge transaction in your wallet. So once you want to spend it, you pay a lot of fees.... am I right?
Setting hourly payout is not a good idea, especially for small amounts. Should avoid keeping many small transactions. Check my answer #2.