Of course L3 forwarding is not by itself "bad" for the packets. However... If you have a network with "excessive" hops (for some definition of excessive), it probably means one or more of the following:
A) you have a poor (or at least non-elegant) network design.
If your L3 topology is well aligned with your L1 topology, you usually end up with more hops. The less intermediate gear, like SONET you use but do L3 instead, the more L3 hops you have.
B) you have more places for things to go wrong in both hardware and software.
This is specifically true for the hop-hiders using MPLS or other mostly pointless multihop recursive switching systems.
C) you're busy gratifying your architectural ego instead of designing the simplest thing possible which gives you the necessary performance and reliability.
Hop-hiding is usually going the other way from the simplest thing.
D) you're buying so much unnecessary hardware that you are either not not financially healthy or you're not passing on as much savings as you could be to your customer.
Eliminating n+1 kinds of gear and replacing it with a smaller number of different kind of boxes makes your network simpler and saves nicely on OPEX. Might be somewhat more CAPEX intensive on the start but not by a large margin.
Now while I'm sure that you don't fit into that definition of "excessive", I can think of a few people who do, and they try to use that "but more L3 hops are never bad" argument.
This would translate to that "hops are bad", regardless of the layer. Many people mess with L4 to L7 generating unneccesary hops on application protocols. These usually seem to be the same growd that does other hiding things. Pete