With Remote Desktop, the application is not actually running on your computers, but on theirs. Your data is there. This implies a lot of things, including:
- In case of loss of network connectivity, business stops.
- If the SaaS provider ceases activity, you lose your tools and your data.
- Any disaster (flood, fire...) affecting the server centre of the SaaS provider will impact you dearly.
- All security decisions with regards to your information assets will be taken by the SaaS provider.
- If you handle data classified as "personal information" then compliance to applicable regulations depends on what the SaaS provider does.
- If your network connectivity is not top notch, especially with a low latency, then your 50 employees will hate the Remote Desktop immensely.
On the other hand:
- Disaster on your site won't harm your data.
- You might benefit from the infrastructures of the provider; e.g., the provider may offer an efficient and comprehensive backup solution for your data.
- You may relocate more easily your premises, and employees may possibly telecommute.
Globally, going SaaS to that level is like marrying a polygamous man: you trust the provider exclusively with your business, but you know that the provider has some interests elsewhere as well.