Mongo HDD disk grows to fast when insert / deleting data
Well. This depends on the below factors. Working Dataset, padding factor and fragmentation. 

You will need to check which of the below things are not working for you.

1) Padding: As you said you implemented padding, can you let me know the value of padding factor of your mongo?

2) Fragmentation leaves some holes in your data files when they are moved around. MongoDB tries to fill holes whenever possible. Again it depends on your data files, if the new data files which are supposed to be accommodated in the existing holes are larger than the hole size, it can't be fit. 
So, compact and usePowerOf2Sizes options come into our rescue. 

Can you let me know the frag value of your collection?

db.(collection).stats().storageSize

It gives the sum of size of the collection + total index size

If you are on MMAPv1, you can switch to WiredTiger storage engine and test how fragmentation is working. You will need to upgrade to 3.0 to plugin to avail this storage engine.

If all the above options doesn't work, we are left with a tough option. Your application has to minimize fragmentation by pre-allocating the max size of a document and ensuring document size growth is managed correctly.