Can I trade in both of my iPads at the same time towards a new iPad?

You can trade-in as many qualifying devices as you wish - either in-store at a physical Apple Store, or using the online trade-in process:

Apple Trade In - Apple

Each device is assessed for eligibility and value in its own right. If using the online trade-in, you’ll only be able to process each device individually - with each device being sent a separate shipping kit. Devices are each returned, assessed and a credit value assigned. The trade-in value is returned to you by way of an Apple gift card for each device - and these can be used to purchase whatever you wish with Apple. 

If a trade-in is initiated during an online purchase, you will usually pay full price for the item - but will receive a refund against your credit card upon subsequent return (and acceptance) of the/each item that was returned for trade-in.

Many choose to complete their trade-in in-store - as doing so facilitates trade-in of multiple items against a single purchase transaction - and removes any uncertainty as to the trade-in value or acceptance.

Check this link...

Apple Trade In - Apple

Apple will let you trade one device towards the purchase of another device. You can however, give Apple additional devices, but for any extra devices, Apple will give you an Apple Gift Card, which you can then use as payment towards something you want.

I suggest you contact Apple directly by clicking on Get Support at upper right corner of any forum page.