1. Yes. STP instances are not started for extra VLANs. This may lead to loops and broadcast storms in these vlans. If you really need so many VLANs and know that some VLANs are loop-free you may disable STP for them ("no spanning-tree vlan X"). This will enable STP for other VLANs (not a good solution though).
2. Yes they can. But this is complex. This works good if your backbone and distribution switches run MST and (some) access switches run PVST+ or 802.1d or RSTP. Following are basic recomendations: 1) configure separate MST instance for backbone VLANs 2) configure separate MST instance for your management VLAN 3) do not use MST instance 0 - move all VLANs to other MST instances 4) to achieve load-balancing configure 2 MST instances for "odd" and "even" access-layer VLANs 5) configure all STP roots to be within your MST region (distribution switches for access-layer VLANs and backbone switch(es) for backbone VLANs) -- never configure STP roots on the PVST+ switches 6) be careful when clearing VLANs from trunks ("sw tr allowed vlan remove ...") -- if you clear - clear all VLANs for the same MST instance 7) configure "spanning-tree vlan cost ..." on the PVST+ access-layer switches to achieve load-balancing if they have two uplinks to the distribution 8) configure all MST switches the same way -- configure all instances and all VLANs under "spanning-tree mst configuration" even if some switch do not have some VLAN or do not pass some VLAN 9) etc. ;)
We are pleased to announce availability of Beta software for 16.6.3. 16.6.3 will be the second rebuild on the 16.6 release train targeted towards Catalyst 9500/9400/9300/3850/3650 switching platforms. We are looking for early feedback from custome...