It will not affect historical transactions by making inventory items inactive but make sure the item has zero quantity before inactivating item. If the item has quantity, make adjust quantity first to zero and then make inactive.
To adjust Inventory Quantity to zero:
From the Gear icon > Lists > Product & Services > Select inventory item in question > Select drop-down arrow (next to Edit under Action column) and Select Adjust Quantity > Make New Quantity to zero and Save. You can also change an Inventory adjustment account field, the default is inventory shrinkage account.