Many people (me included) run more than one filter on certain tanks for many reasons. There is no single reason stating you must or can't do it.
As far as your bacteria goes, yes you lose what is on the pad, however that is not of a majority quantity to cause your tank to recycle. The majority of beneficial bacteria resides on all hard surfaces, i.e. the substrate, the glass, the walls of the filter, etc.
"Filter sizes, should you go larger?" Only you can answer that question. Depending on what you stock and how much, is your deciding factor. If you stock "messy" or "dirty" fish such as Oscars, plecos or goldfish, not only larger but also redundancy is preferred. I look for a flow rate equal to 6 to 10 times an hour turnover of water. For things that have a low bio-demand on the tank system, I will go with a lower rating.
As an example, if I want to filter a 20 gallon tank I may use a filter that has 160gph advertised rating, or I may use one that has a 200gph rating depending on the stock. In the case of my Oscars and plecos (messy fish) I use 2 Marineland Emperor 400's on each end of the 90 gallon tank to help eliminate dead spots ad to suck up as much waste as possible. Doing so gives a combined filtration of approximately 800gph equaling an 8 times an hour turn-over rate. When using the advertised flow rate that gives me a theoretical 7.5 gallons of water each minute filtered.
Do what is right for you and your fish. Keep in mind when a manufacturer states it is good for 30 gallons, it may mean filtering 30 gallons at 4 times an hour or it could be 6-8 times an hour. There is no industry standard for what is an acceptable flow rate.